The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Dynamics of rain-induced pollutographs of solubles in sewers.

PubMed

Rutsch, M; Müller, I; Krebs, P

2005-01-01

When looking at acute receiving water impacts due to combined sewer overflows the characteristics of the background diurnal sewage flux variation may influence the peak loads from combined sewer overflows (CSO) and wastewater treatment plant (WWTP) effluent significantly. In this paper, effects on the dynamic compounds transported in the sewer, on CSO discharges and WWTP loading are evaluated by means of hydrodynamic simulations. The simulations are based on different scenarios for diurnal dry-weather flow variations induced by different infiltration rates.

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

NASA Astrophysics Data System (ADS)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

Dynamical properties of magnetized two-dimensional one-component plasma

NASA Astrophysics Data System (ADS)

Dubey, Girija S.; Gumbs, Godfrey; Fessatidis, Vassilios

2018-05-01

Molecular dynamics simulation are used to examine the effect of a uniform perpendicular magnetic field on a two-dimensional interacting electron system. In this simulation we include the effect of the magnetic field classically through the Lorentz force. Both the Coulomb and the magnetic forces are included directly in the electron dynamics to study their combined effect on the dynamical properties of the 2D system. Results are presented for the velocity autocorrelation function and the diffusion constants in the presence and absence of an external magnetic field. Our simulation results clearly show that the external magnetic field has an effect on the dynamical properties of the system.

Symplectic molecular dynamics simulations on specially designed parallel computers.

PubMed

Borstnik, Urban; Janezic, Dusanka

2005-01-01

We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

PubMed

Medley, J Kyle; Choi, Kiri; König, Matthias; Smith, Lucian; Gu, Stanley; Hellerstein, Joseph; Sealfon, Stuart C; Sauro, Herbert M

2018-06-01

The considerable difficulty encountered in reproducing the results of published dynamical models limits validation, exploration and reuse of this increasingly large biomedical research resource. To address this problem, we have developed Tellurium Notebook, a software system for model authoring, simulation, and teaching that facilitates building reproducible dynamical models and reusing models by 1) providing a notebook environment which allows models, Python code, and narrative to be intermixed, 2) supporting the COMBINE archive format during model development for capturing model information in an exchangeable format and 3) enabling users to easily simulate and edit public COMBINE-compliant models from public repositories to facilitate studying model dynamics, variants and test cases. Tellurium Notebook, a Python-based Jupyter-like environment, is designed to seamlessly inter-operate with these community standards by automating conversion between COMBINE standards formulations and corresponding in-line, human-readable representations. Thus, Tellurium brings to systems biology the strategy used by other literate notebook systems such as Mathematica. These capabilities allow users to edit every aspect of the standards-compliant models and simulations, run the simulations in-line, and re-export to standard formats. We provide several use cases illustrating the advantages of our approach and how it allows development and reuse of models without requiring technical knowledge of standards. Adoption of Tellurium should accelerate model development, reproducibility and reuse.

Analysis of the dynamic behavior of structures using the high-rate GNSS-PPP method combined with a wavelet-neural model: Numerical simulation and experimental tests

NASA Astrophysics Data System (ADS)

Kaloop, Mosbeh R.; Yigit, Cemal O.; Hu, Jong W.

2018-03-01

Recently, the high rate global navigation satellite system-precise point positioning (GNSS-PPP) technique has been used to detect the dynamic behavior of structures. This study aimed to increase the accuracy of the extraction oscillation properties of structural movements based on the high-rate (10 Hz) GNSS-PPP monitoring technique. A developmental model based on the combination of wavelet package transformation (WPT) de-noising and neural network prediction (NN) was proposed to improve the dynamic behavior of structures for GNSS-PPP method. A complicated numerical simulation involving highly noisy data and 13 experimental cases with different loads were utilized to confirm the efficiency of the proposed model design and the monitoring technique in detecting the dynamic behavior of structures. The results revealed that, when combined with the proposed model, GNSS-PPP method can be used to accurately detect the dynamic behavior of engineering structures as an alternative to relative GNSS method.

A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics.

PubMed

Oganesyan, Vasily S; Chami, Fatima; White, Gaye F; Thomson, Andrew J

2017-01-01

EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental and modelling results using two structurally different sites of attachment to Myoglobin show that the EPR spectra of Rn are more sensitive to the local protein environment than that of MTSL. This study reveals the potential of using the Rn spin label as a reporter of protein motions. Copyright © 2016 Elsevier Inc. All rights reserved.

[Computational fluid dynamics simulation of different impeller combinations in high viscosity fermentation and its application].

PubMed

Dong, Shuhao; Zhu, Ping; Xu, Xiaoying; Li, Sha; Jiang, Yongxiang; Xu, Hong

2015-07-01

Agitator is one of the essential factors to realize high efficient fermentation for high aerobic and viscous microorganisms, and the influence of different impeller combination on the fermentation process is very important. Welan gum is a microbial exopolysaccharide produced by Alcaligenes sp. under high aerobic and high viscos conditions. Computational fluid dynamics (CFD) numerical simulation was used for analyzing the distribution of velocity, shear rate and gas holdup in the welan fermentation reactor under six different impeller combinations. The best three combinations of impellers were applied to the fermentation of welan. By analyzing the fermentation performance, the MB-4-6 combination had better effect on dissolved oxygen and velocity. The content of welan was increased by 13%. Furthermore, the viscosity of production were also increased.

A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.

PubMed

Komeiji, Y; Yokoyama, H; Uebayasi, M; Taiji, M; Fukushige, T; Sugimoto, D; Takata, R; Shimizu, A; Itsukashi, K

1996-01-01

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging from the acceptable fluctuation of the total energy. Then a software named PEACH (Program for Energetic Analysis of bioCHemical molecules) was developed for molecular dynamics of biomolecules in combination with MD-GRAPE. Molecular dynamics simulation was performed for several protein-solvent systems with different sizes. Simulation of the largest system investigated (27,000 atoms) took only 5 sec/step. Thus, the PEACH-GRAPE system is expected to be useful in accurate and reliable simulation of large biomolecules.

Study of Nanocomposites of Amino Acids and Organic Polyethers by Means of Mass Spectrometry and Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Zobnina, V. G.; Kosevich, M. V.; Chagovets, V. V.; Boryak, O. A.

A problem of elucidation of structure of nanomaterials based on combination of proteins and polyether polymers is addressed on the monomeric level of single amino acids and oligomers of PEG-400 and OEG-5 polyethers. Efficiency of application of combined approach involving experimental electrospray mass spectrometry and computer modeling by molecular dynamics simulation is demonstrated. It is shown that oligomers of polyethers form stable complexes with amino acids valine, proline, histidine, glutamic, and aspartic acids. Molecular dynamics simulation has shown that stabilization of amino acid-polyether complexes is achieved due to winding of the polymeric chain around charged groups of amino acids. Structural motives revealed for complexes of single amino acids with polyethers can be realized in structures of protein-polyether nanoparticles currently designed for drug delivery.

Swarm Intelligence for Urban Dynamics Modelling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghnemat, Rawan; Bertelle, Cyrille; Duchamp, Gerard H. E.

2009-04-16

In this paper, we propose swarm intelligence algorithms to deal with dynamical and spatial organization emergence. The goal is to model and simulate the developement of spatial centers using multi-criteria. We combine a decentralized approach based on emergent clustering mixed with spatial constraints or attractions. We propose an extension of the ant nest building algorithm with multi-center and adaptive process. Typically, this model is suitable to analyse and simulate urban dynamics like gentrification or the dynamics of the cultural equipment in urban area.

Swarm Intelligence for Urban Dynamics Modelling

NASA Astrophysics Data System (ADS)

Ghnemat, Rawan; Bertelle, Cyrille; Duchamp, Gérard H. E.

2009-04-01

In this paper, we propose swarm intelligence algorithms to deal with dynamical and spatial organization emergence. The goal is to model and simulate the developement of spatial centers using multi-criteria. We combine a decentralized approach based on emergent clustering mixed with spatial constraints or attractions. We propose an extension of the ant nest building algorithm with multi-center and adaptive process. Typically, this model is suitable to analyse and simulate urban dynamics like gentrification or the dynamics of the cultural equipment in urban area.

A Framework for Simulating Turbine-Based Combined-Cycle Inlet Mode-Transition

NASA Technical Reports Server (NTRS)

Le, Dzu K.; Vrnak, Daniel R.; Slater, John W.; Hessel, Emil O.

2012-01-01

A simulation framework based on the Memory-Mapped-Files technique was created to operate multiple numerical processes in locked time-steps and send I/O data synchronously across to one-another to simulate system-dynamics. This simulation scheme is currently used to study the complex interactions between inlet flow-dynamics, variable-geometry actuation mechanisms, and flow-controls in the transition from the supersonic to hypersonic conditions and vice-versa. A study of Mode-Transition Control for a high-speed inlet wind-tunnel model with this MMF-based framework is presented to illustrate this scheme and demonstrate its usefulness in simulating supersonic and hypersonic inlet dynamics and controls or other types of complex systems.

Pressure calculation in hybrid particle-field simulations

NASA Astrophysics Data System (ADS)

Milano, Giuseppe; Kawakatsu, Toshihiro

2010-12-01

In the framework of a recently developed scheme for a hybrid particle-field simulation techniques where self-consistent field (SCF) theory and particle models (molecular dynamics) are combined [J. Chem. Phys. 130, 214106 (2009)], we developed a general formulation for the calculation of instantaneous pressure and stress tensor. The expressions have been derived from statistical mechanical definition of the pressure starting from the expression for the free energy functional in the SCF theory. An implementation of the derived formulation suitable for hybrid particle-field molecular dynamics-self-consistent field simulations is described. A series of test simulations on model systems are reported comparing the calculated pressure with those obtained from standard molecular dynamics simulations based on pair potentials.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Liquid li structure and dynamics: A comparison between OFDFT and second nearest-neighbor embedded-atom method

DOE PAGES

Chen, Mohan; Vella, Joseph R.; Panagiotopoulos, Athanassios Z.; ...

2015-04-08

The structure and dynamics of liquid lithium are studied using two simulation methods: orbital-free (OF) first-principles molecular dynamics (MD), which employs OF density functional theory (DFT), and classical MD utilizing a second nearest-neighbor embedded-atom method potential. The properties we studied include the dynamic structure factor, the self-diffusion coefficient, the dispersion relation, the viscosity, and the bond angle distribution function. Our simulation results were compared to available experimental data when possible. Each method has distinct advantages and disadvantages. For example, OFDFT gives better agreement with experimental dynamic structure factors, yet is more computationally demanding than classical simulations. Classical simulations can accessmore » a broader temperature range and longer time scales. The combination of first-principles and classical simulations is a powerful tool for studying properties of liquid lithium.« less

ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-Level Rule-Based Models in Cell Biology.

PubMed

Bittig, Arne T; Uhrmacher, Adelinde M

2017-01-01

Spatio-temporal dynamics of cellular processes can be simulated at different levels of detail, from (deterministic) partial differential equations via the spatial Stochastic Simulation algorithm to tracking Brownian trajectories of individual particles. We present a spatial simulation approach for multi-level rule-based models, which includes dynamically hierarchically nested cellular compartments and entities. Our approach ML-Space combines discrete compartmental dynamics, stochastic spatial approaches in discrete space, and particles moving in continuous space. The rule-based specification language of ML-Space supports concise and compact descriptions of models and to adapt the spatial resolution of models easily.

Structurally Dynamic Spin Market Networks

NASA Astrophysics Data System (ADS)

Horváth, Denis; Kuscsik, Zoltán

The agent-based model of stock price dynamics on a directed evolving complex network is suggested and studied by direct simulation. The stationary regime is maintained as a result of the balance between the extremal dynamics, adaptivity of strategic variables and reconnection rules. The inherent structure of node agent "brain" is modeled by a recursive neural network with local and global inputs and feedback connections. For specific parametric combination the complex network displays small-world phenomenon combined with scale-free behavior. The identification of a local leader (network hub, agent whose strategies are frequently adapted by its neighbors) is carried out by repeated random walk process through network. The simulations show empirically relevant dynamics of price returns and volatility clustering. The additional emerging aspects of stylized market statistics are Zipfian distributions of fitness.

Space station dynamics, attitude control and momentum management

NASA Technical Reports Server (NTRS)

Sunkel, John W.; Singh, Ramen P.; Vengopal, Ravi

1989-01-01

The Space Station Attitude Control System software test-bed provides a rigorous environment for the design, development and functional verification of GN and C algorithms and software. The approach taken for the simulation of the vehicle dynamics and environmental models using a computationally efficient algorithm is discussed. The simulation includes capabilities for docking/berthing dynamics, prescribed motion dynamics associated with the Mobile Remote Manipulator System (MRMS) and microgravity disturbances. The vehicle dynamics module interfaces with the test-bed through the central Communicator facility which is in turn driven by the Station Control Simulator (SCS) Executive. The Communicator addresses issues such as the interface between the discrete flight software and the continuous vehicle dynamics, and multi-programming aspects such as the complex flow of control in real-time programs. Combined with the flight software and redundancy management modules, the facility provides a flexible, user-oriented simulation platform.

Capstone Teaching Models: Combining Simulation, Analytical Intuitive Learning Processes, History and Effectiveness

ERIC Educational Resources Information Center

Reid, Maurice; Brown, Steve; Tabibzadeh, Kambiz

2012-01-01

For the past decade teaching models have been changing, reflecting the dynamics, complexities, and uncertainties of today's organizations. The traditional and the more current active models of learning have disadvantages. Simulation provides a platform to combine the best aspects of both types of teaching practices. This research explores the…

Molecular dynamics simulations of a K+ channel blocker: Tc1 toxin from Tityus cambridgei.

PubMed

Grottesi, Alessandro; Sansom, Mark S P

2003-01-30

Toxins that block voltage-gated potassium (Kv) channels provide a possible template for improved homology models of the Kv pore. In assessing the interactions of Kv channels and their toxins it is important to determine the dynamic flexibility of the toxins. Multiple 10 ns duration molecular dynamics simulations combined with essential dynamics analysis have been used to explore the flexibility of four different Kv channel-blocking toxins. Three toxins (Tc1, AgTx and ChTx) share a common fold. They also share a common pattern of conformational dynamics, as revealed by essential dynamics analysis of the simulation results. This suggests that some aspects of dynamic behaviour are conserved across a single protein fold class. In each of these three toxins, the residue exhibiting minimum flexibility corresponds to a conserved lysine residue that is suggested to interact with the filter domain of the channel. Thus, comparative simulations reveal functionally important conservation of molecular dynamics as well as protein fold across a family of related toxins.

Continuum Damage Modeling for Dynamic Fracture Toughness of Metal Matrix Composites

NASA Astrophysics Data System (ADS)

Lee, Intaek; Ochi, Yasuo; Bae, Sungin; Song, Jungil

Short fiber reinforced metal-matrix composites (MMCs) have widely adopted as structural materials and many experimental researches have been performed to study fracture toughness of it. Fracture toughness is often referred as the plane strain(maximum constraint) fracture toughness KIc determined by the well-established standard test method, such as ASTM E399. But the application for dynamic fracture toughness KId has not been popular yet, because of reliance in capturing the crack propagating time. This paper deals with dynamic fracture toughness testing and simulation using finite element method to evaluate fracture behaviors of MMCs manufactured by squeeze casting process when material combination is varied with the type of reinforcement (appearance, size), volume fraction and combination of reinforcements, and the matrix alloy. The instrumented Charphy impact test was used for KId determination and continuum damage model embedded in commercial FE program is used to investigate the dynamic fracture toughness with the influence of elasto-visco-plastic constitutive relation of quasi-brittle fracture that is typical examples of ceramics and some fibre reinforced composites. With Compared results between experimental method and FE simulation, the determination process for KId is presented. FE simulation coupled with continuum damage model is emphasized single shot simulation can predict the dynamic fracture toughness, KId and real time evolution of that directly.

General framework for constraints in molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Kneller, Gerald R.

2017-06-01

The article presents a theoretical framework for molecular dynamics simulations of complex systems subject to any combination of holonomic and non-holonomic constraints. Using the concept of constrained inverse matrices both the particle accelerations and the associated constraint forces can be determined from given external forces and kinematical conditions. The formalism enables in particular the construction of explicit kinematical conditions which lead to the well-known Nosé-Hoover type equations of motion for the simulation of non-standard molecular dynamics ensembles. Illustrations are given for a few examples and an outline is presented for a numerical implementation of the method.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less

Dynamic computer simulations of electrophoresis: three decades of active research.

PubMed

Thormann, Wolfgang; Caslavska, Jitka; Breadmore, Michael C; Mosher, Richard A

2009-06-01

Dynamic models for electrophoresis are based upon model equations derived from the transport concepts in solution together with user-inputted conditions. They are able to predict theoretically the movement of ions and are as such the most versatile tool to explore the fundamentals of electrokinetic separations. Since its inception three decades ago, the state of dynamic computer simulation software and its use has progressed significantly and Electrophoresis played a pivotal role in that endeavor as a large proportion of the fundamental and application papers were published in this periodical. Software is available that simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. This has been employed to show the detailed mechanisms of many of the fundamental phenomena that occur in electrophoretic separations. Dynamic electrophoretic simulations are relevant for separations on any scale and instrumental format, including free-fluid preparative, gel, capillary and chip electrophoresis. This review includes a historical overview, a survey of current simulators, simulation examples and a discussion of the applications and achievements of dynamic simulation.

Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Spörlein, Sebastian; Carstens, Heiko; Satzger, Helmut; Renner, Christian; Behrendt, Raymond; Moroder, Luis; Tavan, Paul; Zinth, Wolfgang; Wachtveitl, Josef

2002-06-01

Femtosecond time-resolved spectroscopy on model peptides with built-in light switches combined with computer simulation of light-triggered motions offers an attractive integrated approach toward the understanding of peptide conformational dynamics. It was applied to monitor the light-induced relaxation dynamics occurring on subnanosecond time scales in a peptide that was backbone-cyclized with an azobenzene derivative as optical switch and spectroscopic probe. The femtosecond spectra permit the clear distinguishing and characterization of the subpicosecond photoisomerization of the chromophore, the subsequent dissipation of vibrational energy, and the subnanosecond conformational relaxation of the peptide. The photochemical cis/trans-isomerization of the chromophore and the resulting peptide relaxations have been simulated with molecular dynamics calculations. The calculated reaction kinetics, as monitored by the energy content of the peptide, were found to match the spectroscopic data. Thus we verify that all-atom molecular dynamics simulations can quantitatively describe the subnanosecond conformational dynamics of peptides, strengthening confidence in corresponding predictions for longer time scales.

Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations.

PubMed

Cuendet, Michel A; Tuckerman, Mark E

2014-08-12

In molecular dynamics simulations, most enhanced sampling methods are traditionally associated with one particular estimator to calculate the free energy surface (FES), such as the histogram, the mean force, or the bias potential. Here, we start from the realization that four enhanced sampling methods, metadynamics and well-tempered metadynamics (in their extended Lagrangian form), as well as driven adiabatic free energy dynamics (dAFED) and unified free energy dynamics (UFED), can be used in combination with any of the three above-mentioned FES estimators. We compare the convergence properties of these estimators on the alanine dipeptide and a sodium ion solvation shell. We find that the mean force estimator is superior in all cases. We also show that it can be marginally beneficial to combine information from the histogram and the force, provided that both are of comparable accuracy.

Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kimminau, G; Nagler, B; Higginbotham, A

2008-06-19

Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

Combined micro and macro geodynamic modelling of mantle flow: methods, potentialities and limits.

NASA Astrophysics Data System (ADS)

Faccenda, M.

2015-12-01

Over the last few years, geodynamic simulations aiming at reconstructing the Earth's internal dynamics have increasingly attempted to link processes occurring at the micro (i.e., strain-induced lattice preferred orientation (LPO) of crystal aggregates) and macro scale (2D/3D mantle convection). As a major outcome, such a combined approach results in the prediction of the modelled region's elastic properties that, in turn, can be used to perform seismological synthetic experiments. By comparison with observables, the geodynamic simulations can then be considered as a good numerical analogue of specific tectonic settings, constraining their deep structure and recent tectonic evolution. In this contribution, I will discuss the recent methodologies, potentialities and current limits of combined micro- and macro-flow simulations, with particular attention to convergent margins whose dynamics and deep structure is still the object of extensive studies.

A Nonlinear Dynamical Systems based Model for Stochastic Simulation of Streamflow

NASA Astrophysics Data System (ADS)

Erkyihun, S. T.; Rajagopalan, B.; Zagona, E. A.

2014-12-01

Traditional time series methods model the evolution of the underlying process as a linear or nonlinear function of the autocorrelation. These methods capture the distributional statistics but are incapable of providing insights into the dynamics of the process, the potential regimes, and predictability. This work develops a nonlinear dynamical model for stochastic simulation of streamflows. In this, first a wavelet spectral analysis is employed on the flow series to isolate dominant orthogonal quasi periodic timeseries components. The periodic bands are added denoting the 'signal' component of the time series and the residual being the 'noise' component. Next, the underlying nonlinear dynamics of this combined band time series is recovered. For this the univariate time series is embedded in a d-dimensional space with an appropriate lag T to recover the state space in which the dynamics unfolds. Predictability is assessed by quantifying the divergence of trajectories in the state space with time, as Lyapunov exponents. The nonlinear dynamics in conjunction with a K-nearest neighbor time resampling is used to simulate the combined band, to which the noise component is added to simulate the timeseries. We demonstrate this method by applying it to the data at Lees Ferry that comprises of both the paleo reconstructed and naturalized historic annual flow spanning 1490-2010. We identify interesting dynamics of the signal in the flow series and epochal behavior of predictability. These will be of immense use for water resources planning and management.

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.

A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens

PubMed Central

Bouhaddou, Mehdi; Koch, Rick J.; DiStefano, Matthew S.; Tan, Annie L.; Mertz, Alex E.

2018-01-01

Most cancer cells harbor multiple drivers whose epistasis and interactions with expression context clouds drug and drug combination sensitivity prediction. We constructed a mechanistic computational model that is context-tailored by omics data to capture regulation of stochastic proliferation and death by pan-cancer driver pathways. Simulations and experiments explore how the coordinated dynamics of RAF/MEK/ERK and PI-3K/AKT kinase activities in response to synergistic mitogen or drug combinations control cell fate in a specific cellular context. In this MCF10A cell context, simulations suggest that synergistic ERK and AKT inhibitor-induced death is likely mediated by BIM rather than BAD, which is supported by prior experimental studies. AKT dynamics explain S-phase entry synergy between EGF and insulin, but simulations suggest that stochastic ERK, and not AKT, dynamics seem to drive cell-to-cell proliferation variability, which in simulations is predictable from pre-stimulus fluctuations in C-Raf/B-Raf levels. Simulations suggest MEK alteration negligibly influences transformation, consistent with clinical data. Tailoring the model to an alternate cell expression and mutation context, a glioma cell line, allows prediction of increased sensitivity of cell death to AKT inhibition. Our model mechanistically interprets context-specific landscapes between driver pathways and cell fates, providing a framework for designing more rational cancer combination therapy. PMID:29579036

Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics

NASA Astrophysics Data System (ADS)

Tao, Xuecheng; Shushkov, Philip; Miller, Thomas F.

2018-03-01

We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is introduced such that Boltzmann sampling of the isomorphic Hamiltonian with classical nuclear degrees of freedom yields the exact quantum Boltzmann distribution for the original physical system. In the limit of a single electronic energy level, the isomorphic Hamiltonian reduces to the familiar cases of either ring polymer molecular dynamics (RPMD) or centroid molecular dynamics Hamiltonians, depending on the implementation. An advantage of the isomorphic Hamiltonian is that it can easily be combined with existing mixed quantum-classical dynamics methods, such as surface hopping or Ehrenfest dynamics, to enable the simulation of electronically non-adiabatic processes with nuclear quantum effects. We present numerical applications of the isomorphic Hamiltonian to model two- and three-level systems, with encouraging results that include improvement upon a previously reported combination of RPMD with surface hopping in the deep-tunneling regime.

Dynamic modelling of an adsorption storage tank using a hybrid approach combining computational fluid dynamics and process simulation

USGS Publications Warehouse

Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.

2004-01-01

A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.

Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions.

PubMed

Li, Hui; Li, Wei; Li, Shuhua; Ma, Jing

2008-06-12

Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.

ChainMail based neural dynamics modeling of soft tissue deformation for surgical simulation.

PubMed

Zhang, Jinao; Zhong, Yongmin; Smith, Julian; Gu, Chengfan

2017-07-20

Realistic and real-time modeling and simulation of soft tissue deformation is a fundamental research issue in the field of surgical simulation. In this paper, a novel cellular neural network approach is presented for modeling and simulation of soft tissue deformation by combining neural dynamics of cellular neural network with ChainMail mechanism. The proposed method formulates the problem of elastic deformation into cellular neural network activities to avoid the complex computation of elasticity. The local position adjustments of ChainMail are incorporated into the cellular neural network as the local connectivity of cells, through which the dynamic behaviors of soft tissue deformation are transformed into the neural dynamics of cellular neural network. Experiments demonstrate that the proposed neural network approach is capable of modeling the soft tissues' nonlinear deformation and typical mechanical behaviors. The proposed method not only improves ChainMail's linear deformation with the nonlinear characteristics of neural dynamics but also enables the cellular neural network to follow the principle of continuum mechanics to simulate soft tissue deformation.

A Novel Interfacing Technique for Distributed Hybrid Simulations Combining EMT and Transient Stability Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shu, Dewu; Xie, Xiaorong; Jiang, Qirong

With steady increase of power electronic devices and nonlinear dynamic loads in large scale AC/DC systems, the traditional hybrid simulation method, which incorporates these components into a single EMT subsystem and hence causes great difficulty for network partitioning and significant deterioration in simulation efficiency. To resolve these issues, a novel distributed hybrid simulation method is proposed in this paper. The key to realize this method is a distinct interfacing technique, which includes: i) a new approach based on the two-level Schur complement to update the interfaces by taking full consideration of the couplings between different EMT subsystems; and ii) amore » combined interaction protocol to further improve the efficiency while guaranteeing the simulation accuracy. The advantages of the proposed method in terms of both efficiency and accuracy have been verified by using it for the simulation study of an AC/DC hybrid system including a two-terminal VSC-HVDC and nonlinear dynamic loads.« less

An atomistic simulation scheme for modeling crystal formation from solution.

PubMed

Kawska, Agnieszka; Brickmann, Jürgen; Kniep, Rüdiger; Hochrein, Oliver; Zahn, Dirk

2006-01-14

We present an atomistic simulation scheme for investigating crystal growth from solution. Molecular-dynamics simulation studies of such processes typically suffer from considerable limitations concerning both system size and simulation times. In our method this time-length scale problem is circumvented by an iterative scheme which combines a Monte Carlo-type approach for the identification of ion adsorption sites and, after each growth step, structural optimization of the ion cluster and the solvent by means of molecular-dynamics simulation runs. An important approximation of our method is based on assuming full structural relaxation of the aggregates between each of the growth steps. This concept only holds for compounds of low solubility. To illustrate our method we studied CaF2 aggregate growth from aqueous solution, which may be taken as prototypes for compounds of very low solubility. The limitations of our simulation scheme are illustrated by the example of NaCl aggregation from aqueous solution, which corresponds to a solute/solvent combination of very high salt solubility.

Longitudinal train dynamics: an overview

NASA Astrophysics Data System (ADS)

Wu, Qing; Spiryagin, Maksym; Cole, Colin

2016-12-01

This paper discusses the evolution of longitudinal train dynamics (LTD) simulations, which covers numerical solvers, vehicle connection systems, air brake systems, wagon dumper systems and locomotives, resistance forces and gravitational components, vehicle in-train instabilities, and computing schemes. A number of potential research topics are suggested, such as modelling of friction, polymer, and transition characteristics for vehicle connection simulations, studies of wagon dumping operations, proper modelling of vehicle in-train instabilities, and computing schemes for LTD simulations. Evidence shows that LTD simulations have evolved with computing capabilities. Currently, advanced component models that directly describe the working principles of the operation of air brake systems, vehicle connection systems, and traction systems are available. Parallel computing is a good solution to combine and simulate all these advanced models. Parallel computing can also be used to conduct three-dimensional long train dynamics simulations.

Computational Methods for Dynamic Stability and Control Derivatives

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Spence, Angela M.; Murphy, Patrick C.

2003-01-01

Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.

Computational Methods for Dynamic Stability and Control Derivatives

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Spence, Angela M.; Murphy, Patrick C.

2004-01-01

Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.

Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics

PubMed Central

2017-01-01

The protein mediated hydrolysis of nucleoside triphosphates such as ATP or GTP is one of the most important and challenging biochemical reactions in nature. The chemical environment (water structure, catalytic metal, and amino acid residues) adjacent to the hydrolysis site contains hundreds of atoms, usually greatly limiting the amount of the free energy sampling that one can achieve from computationally demanding electronic structure calculations such as QM/MM simulations. Therefore, the combination of QM/MM molecular dynamics with the recently developed transition-tempered metadynamics (TTMetaD), an enhanced sampling method that can provide a high-quality free energy estimate at an early stage in a simulation, is an ideal approach to address the biomolecular nucleoside triphosphate hydrolysis problem. In this work the ATP hydrolysis process in monomeric and filamentous actin is studied as an example application of the combined methodology. The performance of TTMetaD in these demanding QM/MM simulations is compared with that of the more conventional well-tempered metadynamics (WTMetaD). Our results show that TTMetaD exhibits much better exploration of the hydrolysis reaction free energy surface in two key collective variables (CVs) during the early stages of the QM/MM simulation than does WTMetaD. The TTMetaD simulations also reveal that a key third degree of freedom, the O–H bond-breaking and proton transfer from the lytic water, must be biased for TTMetaD to converge fully. To perturb the NTP hydrolysis dynamics to the least extent and to properly focus the MetaD free energy sampling, we also adopt here the recently developed metabasin metadynamics (MBMetaD) to construct a self-limiting bias potential that only applies to the lytic water after its nucleophilic attack of the phosphate of ATP. With these new, state-of-the-art enhanced sampling metadynamics techniques, we present an effective and accurate computational strategy for combining QM/MM molecular dynamics simulation with free energy sampling methodology, including a means to analyze the convergence of the calculations through robust numerical criteria. PMID:28345907

Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics.

PubMed

Sun, Rui; Sode, Olaseni; Dama, James F; Voth, Gregory A

2017-05-09

The protein mediated hydrolysis of nucleoside triphosphates such as ATP or GTP is one of the most important and challenging biochemical reactions in nature. The chemical environment (water structure, catalytic metal, and amino acid residues) adjacent to the hydrolysis site contains hundreds of atoms, usually greatly limiting the amount of the free energy sampling that one can achieve from computationally demanding electronic structure calculations such as QM/MM simulations. Therefore, the combination of QM/MM molecular dynamics with the recently developed transition-tempered metadynamics (TTMetaD), an enhanced sampling method that can provide a high-quality free energy estimate at an early stage in a simulation, is an ideal approach to address the biomolecular nucleoside triphosphate hydrolysis problem. In this work the ATP hydrolysis process in monomeric and filamentous actin is studied as an example application of the combined methodology. The performance of TTMetaD in these demanding QM/MM simulations is compared with that of the more conventional well-tempered metadynamics (WTMetaD). Our results show that TTMetaD exhibits much better exploration of the hydrolysis reaction free energy surface in two key collective variables (CVs) during the early stages of the QM/MM simulation than does WTMetaD. The TTMetaD simulations also reveal that a key third degree of freedom, the O-H bond-breaking and proton transfer from the lytic water, must be biased for TTMetaD to converge fully. To perturb the NTP hydrolysis dynamics to the least extent and to properly focus the MetaD free energy sampling, we also adopt here the recently developed metabasin metadynamics (MBMetaD) to construct a self-limiting bias potential that only applies to the lytic water after its nucleophilic attack of the phosphate of ATP. With these new, state-of-the-art enhanced sampling metadynamics techniques, we present an effective and accurate computational strategy for combining QM/MM molecular dynamics simulation with free energy sampling methodology, including a means to analyze the convergence of the calculations through robust numerical criteria.

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments

NASA Astrophysics Data System (ADS)

Brodeck, M.; Alvarez, F.; Arbe, A.; Juranyi, F.; Unruh, T.; Holderer, O.; Colmenero, J.; Richter, D.

2009-03-01

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below ≈0.6 Å-1. We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments.

PubMed

Brodeck, M; Alvarez, F; Arbe, A; Juranyi, F; Unruh, T; Holderer, O; Colmenero, J; Richter, D

2009-03-07

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below approximately 0.6 A(-1). We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Simulating Vibrations in a Complex Loaded Structure

NASA Technical Reports Server (NTRS)

Cao, Tim T.

2005-01-01

The Dynamic Response Computation (DIRECT) computer program simulates vibrations induced in a complex structure by applied dynamic loads. Developed to enable rapid analysis of launch- and landing- induced vibrations and stresses in a space shuttle, DIRECT also can be used to analyze dynamic responses of other structures - for example, the response of a building to an earthquake, or the response of an oil-drilling platform and attached tanks to large ocean waves. For a space-shuttle simulation, the required input to DIRECT includes mathematical models of the space shuttle and its payloads, and a set of forcing functions that simulates launch and landing loads. DIRECT can accommodate multiple levels of payload attachment and substructure as well as nonlinear dynamic responses of structural interfaces. DIRECT combines the shuttle and payload models into a single structural model, to which the forcing functions are then applied. The resulting equations of motion are reduced to an optimum set and decoupled into a unique format for simulating dynamics. During the simulation, maximum vibrations, loads, and stresses are monitored and recorded for subsequent analysis to identify structural deficiencies in the shuttle and/or payloads.

Probability Simulations by Non-Lipschitz Chaos

NASA Technical Reports Server (NTRS)

Zak, Michail

1996-01-01

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

A size-composition resolved aerosol model for simulating the dynamics of externally mixed particles: SCRAM (v 1.0)

NASA Astrophysics Data System (ADS)

Zhu, S.; Sartelet, K. N.; Seigneur, C.

2015-06-01

The Size-Composition Resolved Aerosol Model (SCRAM) for simulating the dynamics of externally mixed atmospheric particles is presented. This new model classifies aerosols by both composition and size, based on a comprehensive combination of all chemical species and their mass-fraction sections. All three main processes involved in aerosol dynamics (coagulation, condensation/evaporation and nucleation) are included. The model is first validated by comparison with a reference solution and with results of simulations using internally mixed particles. The degree of mixing of particles is investigated in a box model simulation using data representative of air pollution in Greater Paris. The relative influence on the mixing state of the different aerosol processes (condensation/evaporation, coagulation) and of the algorithm used to model condensation/evaporation (bulk equilibrium, dynamic) is studied.

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

PubMed

Ostermeir, Katja; Zacharias, Martin

2014-12-01

Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations. © 2014 Wiley Periodicals, Inc.

Microsecond Simulations of DNA and Ion Transport in Nanopores with Novel Ion-Ion and Ion-Nucleotides Effective Potentials

PubMed Central

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei

2014-01-01

We developed a novel scheme based on the Grand-Canonical Monte-Carlo/Brownian Dynamics (GCMC/BD) simulations and have extended it to studies of ion currents across three nanopores with the potential for ssDNA sequencing: solid-state nanopore Si3N4, α-hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide-specific ion dynamics compatible with ssDNA coarse-grained model, we used the Inverse Monte-Carlo protocol, which maps the relevant ion-nucleotide distribution functions from an all-atom MD simulations. Combined with the previously developed simulation platform for Brownian Dynamic (BD) simulations of ion transport, it allows for microsecond- and millisecond-long simulations of ssDNA dynamics in nanopore with a conductance computation accuracy that equals or exceeds that of all-atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all-atom MD simulations. PMID:24738152

Using simulation to interpret experimental data in terms of protein conformational ensembles.

PubMed

Allison, Jane R

2017-04-01

In their biological environment, proteins are dynamic molecules, necessitating an ensemble structural description. Molecular dynamics simulations and solution-state experiments provide complimentary information in the form of atomically detailed coordinates and averaged or distributions of structural properties or related quantities. Recently, increases in the temporal and spatial scale of conformational sampling and comparison of the more diverse conformational ensembles thus generated have revealed the importance of sampling rare events. Excitingly, new methods based on maximum entropy and Bayesian inference are promising to provide a statistically sound mechanism for combining experimental data with molecular dynamics simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Robust, nonlinear, high angle-of-attack control design for a supermaneuverable vehicle

NASA Technical Reports Server (NTRS)

Adams, Richard J.

1993-01-01

High angle-of-attack flight control laws are developed for a supermaneuverable fighter aircraft. The methods of dynamic inversion and structured singular value synthesis are combined into an approach which addresses both the nonlinearity and robustness problems of flight at extreme operating conditions. The primary purpose of the dynamic inversion control elements is to linearize the vehicle response across the flight envelope. Structured singular value synthesis is used to design a dynamic controller which provides robust tracking to pilot commands. The resulting control system achieves desired flying qualities and guarantees a large margin of robustness to uncertainties for high angle-of-attack flight conditions. The results of linear simulation and structured singular value stability analysis are presented to demonstrate satisfaction of the design criteria. High fidelity nonlinear simulation results show that the combined dynamics inversion/structured singular value synthesis control law achieves a high level of performance in a realistic environment.

Hybrid particle-continuum simulations coupling Brownian dynamics and local dynamic density functional theory.

PubMed

Qi, Shuanhu; Schmid, Friederike

2017-11-08

We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense such that particles can switch their level of resolution on the fly. The switching of resolution is controlled by a tuning function which can be chosen at will according to the geometry of the system. As an application, the hybrid scheme is used to study the kinetics of interfacial broadening of a polymer blend, and is validated by comparing the results to the predictions from pure Brownian dynamics and pure local dynamics calculations.

Dispersion of response times reveals cognitive dynamics.

PubMed

Holden, John G; Van Orden, Guy C; Turvey, Michael T

2009-04-01

Trial-to-trial variation in word-pronunciation times exhibits 1/f scaling. One explanation is that human performances are consequent on multiplicative interactions among interdependent processes-interaction dominant dynamics. This article describes simulated distributions of pronunciation times in a further test for multiplicative interactions and interdependence. Individual participant distributions of approximately 1,100 word-pronunciation times were successfully mimicked for each participant in combinations of lognormal and power-law behavior. Successful hazard function simulations generalized these results to establish interaction dominant dynamics, in contrast with component dominant dynamics, as a likely mechanism for cognitive activity. (c) 2009 APA, all rights reserved

Dispersion of Response Times Reveals Cognitive Dynamics

PubMed Central

Holden, John G.; Van Orden, Guy C.; Turvey, Michael T.

2013-01-01

Trial to trial variation in word pronunciation times exhibits 1/f scaling. One explanation is that human performances are consequent on multiplicative interactions among interdependent processes – interaction dominant dynamics. This article describes simulated distributions of pronunciation times in a further test for multiplicative interactions and interdependence. Individual participant distributions of ≈1100 word pronunciation times are successfully mimicked for each participant in combinations of lognormal and power law behavior. Successful hazard function simulations generalize these results to establish interaction dominant dynamics, in contrast with component dominant dynamics, as a likely mechanism for cognitive activity. PMID:19348544

Medicinal plant phytochemicals and their inhibitory activities against pancreatic lipase: molecular docking combined with molecular dynamics simulation approach.

PubMed

Ahmed, Bilal; Ali Ashfaq, Usman; Usman Mirza, Muhammad

2018-05-01

Obesity is the worst health risk worldwide, which is linked to a number of diseases. Pancreatic lipase is considered as an affective cause of obesity and can be a major target for controlling the obesity. The present study was designed to find out best phytochemicals against pancreatic lipase through molecular docking combined with molecular dynamics (MD) simulation. For this purpose, a total of 3770 phytochemicals were docked against pancreatic lipase and ranked them on the basis of binding affinity. Finally, 10 molecules (Kushenol K, Rosmarinic acid, Reserpic acid, Munjistin, Leachianone G, Cephamycin C, Arctigenin, 3-O-acetylpadmatin, Geniposide and Obtusin) were selected that showed strong bonding with the pancreatic lipase. MD simulations were performed on top five compounds using AMBER16. The simulated complexes revealed stability and ligands remained inside the binding pocket. This study concluded that these finalised molecules can be used as drug candidate to control obesity.

A Decision Tool that Combines Discrete Event Software Process Models with System Dynamics Pieces for Software Development Cost Estimation and Analysis

NASA Technical Reports Server (NTRS)

Mizell, Carolyn Barrett; Malone, Linda

2007-01-01

The development process for a large software development project is very complex and dependent on many variables that are dynamic and interrelated. Factors such as size, productivity and defect injection rates will have substantial impact on the project in terms of cost and schedule. These factors can be affected by the intricacies of the process itself as well as human behavior because the process is very labor intensive. The complex nature of the development process can be investigated with software development process models that utilize discrete event simulation to analyze the effects of process changes. The organizational environment and its effects on the workforce can be analyzed with system dynamics that utilizes continuous simulation. Each has unique strengths and the benefits of both types can be exploited by combining a system dynamics model and a discrete event process model. This paper will demonstrate how the two types of models can be combined to investigate the impacts of human resource interactions on productivity and ultimately on cost and schedule.

Simulations of Probabilities for Quantum Computing

NASA Technical Reports Server (NTRS)

Zak, M.

1996-01-01

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

Integrating neuroinformatics tools in TheVirtualBrain.

PubMed

Woodman, M Marmaduke; Pezard, Laurent; Domide, Lia; Knock, Stuart A; Sanz-Leon, Paula; Mersmann, Jochen; McIntosh, Anthony R; Jirsa, Viktor

2014-01-01

TheVirtualBrain (TVB) is a neuroinformatics Python package representing the convergence of clinical, systems, and theoretical neuroscience in the analysis, visualization and modeling of neural and neuroimaging dynamics. TVB is composed of a flexible simulator for neural dynamics measured across scales from local populations to large-scale dynamics measured by electroencephalography (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI), and core analytic and visualization functions, all accessible through a web browser user interface. A datatype system modeling neuroscientific data ties together these pieces with persistent data storage, based on a combination of SQL and HDF5. These datatypes combine with adapters allowing TVB to integrate other algorithms or computational systems. TVB provides infrastructure for multiple projects and multiple users, possibly participating under multiple roles. For example, a clinician might import patient data to identify several potential lesion points in the patient's connectome. A modeler, working on the same project, tests these points for viability through whole brain simulation, based on the patient's connectome, and subsequent analysis of dynamical features. TVB also drives research forward: the simulator itself represents the culmination of several simulation frameworks in the modeling literature. The availability of the numerical methods, set of neural mass models and forward solutions allows for the construction of a wide range of brain-scale simulation scenarios. This paper briefly outlines the history and motivation for TVB, describing the framework and simulator, giving usage examples in the web UI and Python scripting.

Integrating neuroinformatics tools in TheVirtualBrain

PubMed Central

Woodman, M. Marmaduke; Pezard, Laurent; Domide, Lia; Knock, Stuart A.; Sanz-Leon, Paula; Mersmann, Jochen; McIntosh, Anthony R.; Jirsa, Viktor

2014-01-01

TheVirtualBrain (TVB) is a neuroinformatics Python package representing the convergence of clinical, systems, and theoretical neuroscience in the analysis, visualization and modeling of neural and neuroimaging dynamics. TVB is composed of a flexible simulator for neural dynamics measured across scales from local populations to large-scale dynamics measured by electroencephalography (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI), and core analytic and visualization functions, all accessible through a web browser user interface. A datatype system modeling neuroscientific data ties together these pieces with persistent data storage, based on a combination of SQL and HDF5. These datatypes combine with adapters allowing TVB to integrate other algorithms or computational systems. TVB provides infrastructure for multiple projects and multiple users, possibly participating under multiple roles. For example, a clinician might import patient data to identify several potential lesion points in the patient's connectome. A modeler, working on the same project, tests these points for viability through whole brain simulation, based on the patient's connectome, and subsequent analysis of dynamical features. TVB also drives research forward: the simulator itself represents the culmination of several simulation frameworks in the modeling literature. The availability of the numerical methods, set of neural mass models and forward solutions allows for the construction of a wide range of brain-scale simulation scenarios. This paper briefly outlines the history and motivation for TVB, describing the framework and simulator, giving usage examples in the web UI and Python scripting. PMID:24795617

XNsim: Internet-Enabled Collaborative Distributed Simulation via an Extensible Network

NASA Technical Reports Server (NTRS)

Novotny, John; Karpov, Igor; Zhang, Chendi; Bedrossian, Nazareth S.

2007-01-01

In this paper, the XNsim approach to achieve Internet-enabled, dynamically scalable collaborative distributed simulation capabilities is presented. With this approach, a complete simulation can be assembled from shared component subsystems written in different formats, that run on different computing platforms, with different sampling rates, in different geographic locations, and over singlelmultiple networks. The subsystems interact securely with each other via the Internet. Furthermore, the simulation topology can be dynamically modified. The distributed simulation uses a combination of hub-and-spoke and peer-topeer network topology. A proof-of-concept demonstrator is also presented. The XNsim demonstrator can be accessed at http://www.jsc.draver.corn/xn that hosts various examples of Internet enabled simulations.

Dynamic modeling and simulation of an integral bipropellant propulsion double-valve combined test system

NASA Astrophysics Data System (ADS)

Chen, Yang; Wang, Huasheng; Xia, Jixia; Cai, Guobiao; Zhang, Zhenpeng

2017-04-01

For the pressure reducing regulator and check valve double-valve combined test system in an integral bipropellant propulsion system, a system model is established with modular models of various typical components. The simulation research is conducted on the whole working process of an experiment of 9 MPa working condition from startup to rated working condition and finally to shutdown. Comparison of simulation results with test data shows: five working conditions including standby, startup, rated pressurization, shutdown and halt and nine stages of the combined test system are comprehensively disclosed; valve-spool opening and closing details of the regulator and two check valves are accurately revealed; the simulation also clarifies two phenomena which test data are unable to clarify, one is the critical opening state in which the check valve spools slightly open and close alternately in their own fully closed positions, the other is the obvious effects of flow-field temperature drop and temperature rise in pipeline network with helium gas flowing. Moreover, simulation results with consideration of component wall heat transfer are closer to the test data than those under the adiabatic-wall condition, and more able to reveal the dynamic characteristics of the system in various working stages.

Generic process design and control strategies used to develop a dynamic model and training software for an IGCC plant with CO2 sequestration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Provost, G.; Stone, H.; McClintock, M.

2008-01-01

To meet the growing demand for education and experience with the analysis, operation, and control of commercial-scale Integrated Gasification Combined Cycle (IGCC) plants, the Department of Energy’s (DOE) National Energy Technology Laboratory (NETL) is leading a collaborative R&D project with participants from government, academia, and industry. One of the goals of this project is to develop a generic, full-scope, real-time generic IGCC dynamic plant simulator for use in establishing a world-class research and training center, as well as to promote and demonstrate the technology to power industry personnel. The NETL IGCC dynamic plant simulator will combine for the first timemore » a process/gasification simulator and a power/combined-cycle simulator together in a single dynamic simulation framework for use in training applications as well as engineering studies. As envisioned, the simulator will have the following features and capabilities: A high-fidelity, real-time, dynamic model of process-side (gasification and gas cleaning with CO2 capture) and power-block-side (combined cycle) for a generic IGCC plant fueled by coal and/or petroleum coke Full-scope training simulator capabilities including startup, shutdown, load following and shedding, response to fuel and ambient condition variations, control strategy analysis (turbine vs. gasifier lead, etc.), representative malfunctions/trips, alarms, scenarios, trending, snapshots, data historian, and trainee performance monitoring The ability to enhance and modify the plant model to facilitate studies of changes in plant configuration and equipment and to support future R&D efforts To support this effort, process descriptions and control strategies were developed for key sections of the plant as part of the detailed functional specification, which will form the basis of the simulator development. These plant sections include: Slurry Preparation Air Separation Unit Gasifiers Syngas Scrubbers Shift Reactors Gas Cooling, Medium Pressure (MP) and Low Pressure (LP) Steam Generation, and Knockout Sour Water Stripper Mercury Removal Selexol™ Acid Gas Removal System CO2 Compression Syngas Reheat and Expansion Claus Plant Hydrogenation Reactor and Gas Cooler Combustion Turbine (CT)-Generator Assemblies Heat Recovery Steam Generators (HRSGs) and Steam Turbine (ST)-Generator In this paper, process descriptions, control strategies, and Process & Instrumentation Diagram (P&ID) drawings for key sections of the generic IGCC plant are presented, along with discussions of some of the operating procedures and representative faults that the simulator will cover. Some of the intended future applications for the simulator are discussed, including plant operation and control demonstrations as well as education and training services such as IGCC familiarization courses.« less

A framework for stochastic simulations and visualization of biological electron-transfer dynamics

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

2015-08-01

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

Quantum Dynamics in Biological Systems

NASA Astrophysics Data System (ADS)

Shim, Sangwoo

In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

Consistent kinetic simulation of plasma and sputtering in low temperature plasmas

NASA Astrophysics Data System (ADS)

Schmidt, Frederik; Trieschmann, Jan; Mussenbrock, Thomas

2016-09-01

Plasmas are commonly used in sputtering applications for the deposition of thin films. Although magnetron sources are a prominent choice, capacitively coupled plasmas have certain advantages (e.g., sputtering of non-conducting and/or ferromagnetic materials, aside of excellent control of the ion energy distribution). In order to understand the collective plasma and sputtering dynamics, a kinetic simulation model is helpful. Particle-in-Cell has been proven to be successful in simulating the plasma dynamics, while the Test-Multi-Particle-Method can be used to describe the sputtered neutral species. In this talk a consistent combination of these methods is presented by consistently coupling the simulated ion flux as input to a neutral particle transport model. The combined model is used to simulate and discuss the spatially dependent densities, fluxes and velocity distributions of all particles. This work is supported by the German Research Foundation (DFG) in the frame of Transregional Collaborative Research Center (SFB) TR-87.

Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoover, W. G.; Hoover, C. G.

1993-08-01

Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

AVESTAR Center for Operational Excellence of Electricity Generation Plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zitney, Stephen

2012-08-29

To address industry challenges in attaining operational excellence for electricity generation plants, the U.S. Department of Energy’s (DOE) National Energy Technology Laboratory (NETL) has launched a world-class facility for Advanced Virtual Energy Simulation Training and Research (AVESTARTM). This presentation will highlight the AVESTARTM Center simulators, facilities, and comprehensive training, education, and research programs focused on the operation and control of high-efficiency, near-zero-emission electricity generation plants. The AVESTAR Center brings together state-of-the-art, real-time, high-fidelity dynamic simulators with full-scope operator training systems (OTSs) and 3D virtual immersive training systems (ITSs) into an integrated energy plant and control room environment. AVESTAR’s initial offeringmore » combines--for the first time--a “gasification with CO2 capture” process simulator with a “combined-cycle” power simulator together in a single OTS/ITS solution for an integrated gasification combined cycle (IGCC) power plant with carbon dioxide (CO2) capture. IGCC systems are an attractive technology option for power generation, especially when capturing and storing CO2 is necessary to satisfy emission targets. The AVESTAR training program offers a variety of courses that merge classroom learning, simulator-based OTS learning in a control-room operations environment, and immersive learning in the interactive 3D virtual plant environment or ITS. All of the courses introduce trainees to base-load plant operation, control, startups, and shutdowns. Advanced courses require participants to become familiar with coordinated control, fuel switching, power-demand load shedding, and load following, as well as to problem solve equipment and process malfunctions. Designed to ensure work force development, training is offered for control room and plant field operators, as well as engineers and managers. Such comprehensive simulator-based instruction allows for realistic training without compromising worker, equipment, and environmental safety. It also better prepares operators and engineers to manage the plant closer to economic constraints while minimizing or avoiding the impact of any potentially harmful, wasteful, or inefficient events. The AVESTAR Center is also used to augment graduate and undergraduate engineering education in the areas of process simulation, dynamics, control, and safety. Students and researchers gain hands-on simulator-based training experience and learn how the commercial-scale power plants respond dynamically to changes in manipulated inputs, such as coal feed flow rate and power demand. Students also analyze how the regulatory control system impacts power plant performance and stability. In addition, students practice start-up, shutdown, and malfunction scenarios. The 3D virtual ITSs are used for plant familiarization, walk-through, equipment animations, and safety scenarios. To further leverage the AVESTAR facilities and simulators, NETL and its university partners are pursuing an innovative and collaborative R&D program. In the area of process control, AVESTAR researchers are developing enhanced strategies for regulatory control and coordinated plant-wide control, including gasifier and gas turbine lead, as well as advanced process control using model predictive control (MPC) techniques. Other AVESTAR R&D focus areas include high-fidelity equipment modeling using partial differential equations, dynamic reduced order modeling, optimal sensor placement, 3D virtual plant simulation, and modern grid. NETL and its partners plan to continue building the AVESTAR portfolio of dynamic simulators, immersive training systems, and advanced research capabilities to satisfy industry’s growing need for training and experience with the operation and control of clean energy plants. Future dynamic simulators under development include natural gas combined cycle (NGCC) and supercritical pulverized coal (SCPC) plants with post-combustion CO2 capture. These dynamic simulators are targeted for use in establishing a Virtual Carbon Capture Center (VCCC), similar in concept to the DOE’s National Carbon Capture Center for slipstream testing. The VCCC will enable developers of CO2 capture technologies to integrate, test, and optimize the operation of their dynamic capture models within the context of baseline power plant dynamic models. The objective is to provide hands-on, simulator-based “learn-by-operating” test platforms to accelerate the scale-up and deployment of CO2 capture technologies. Future AVESTAR plans also include pursuing R&D on the dynamics, operation, and control of integrated electricity generation and storage systems for the modern grid era. Special emphasis will be given to combining load-following energy plants with renewable and distributed generating supplies and fast-ramping energy storage systems to provide near constant baseload power.« less

Girsanov reweighting for path ensembles and Markov state models

NASA Astrophysics Data System (ADS)

Donati, L.; Hartmann, C.; Keller, B. G.

2017-06-01

The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules. We present a method to obtain path ensemble averages of a perturbed dynamics from a set of paths generated by a reference dynamics. It is based on the concept of path probability measure and the Girsanov theorem, a result from stochastic analysis to estimate a change of measure of a path ensemble. Since Markov state models (MSMs) of the molecular dynamics can be formulated as a combined phase-space and path ensemble average, the method can be extended to reweight MSMs by combining it with a reweighting of the Boltzmann distribution. We demonstrate how to efficiently implement the Girsanov reweighting in a molecular dynamics simulation program by calculating parts of the reweighting factor "on the fly" during the simulation, and we benchmark the method on test systems ranging from a two-dimensional diffusion process and an artificial many-body system to alanine dipeptide and valine dipeptide in implicit and explicit water. The method can be used to study the sensitivity of molecular dynamics on external perturbations as well as to reweight trajectories generated by enhanced sampling schemes to the original dynamics.

Cyber Physical System Modelling of Distribution Power Systems for Dynamic Demand Response

NASA Astrophysics Data System (ADS)

Chu, Xiaodong; Zhang, Rongxiang; Tang, Maosen; Huang, Haoyi; Zhang, Lei

2018-01-01

Dynamic demand response (DDR) is a package of control methods to enhance power system security. A CPS modelling and simulation platform for DDR in distribution power systems is presented in this paper. CPS modelling requirements of distribution power systems are analyzed. A coupled CPS modelling platform is built for assessing DDR in the distribution power system, which combines seamlessly modelling tools of physical power networks and cyber communication networks. Simulations results of IEEE 13-node test system demonstrate the effectiveness of the modelling and simulation platform.

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

PubMed

Bottaro, Sandro; Bussi, Giovanni; Kennedy, Scott D; Turner, Douglas H; Lindorff-Larsen, Kresten

2018-05-01

RNA molecules are key players in numerous cellular processes and are characterized by a complex relationship between structure, dynamics, and function. Despite their apparent simplicity, RNA oligonucleotides are very flexible molecules, and understanding their internal dynamics is particularly challenging using experimental data alone. We show how to reconstruct the conformational ensemble of four RNA tetranucleotides by combining atomistic molecular dynamics simulations with nuclear magnetic resonance spectroscopy data. The goal is achieved by reweighting simulations using a maximum entropy/Bayesian approach. In this way, we overcome problems of current simulation methods, as well as in interpreting ensemble- and time-averaged experimental data. We determine the populations of different conformational states by considering several nuclear magnetic resonance parameters and point toward properties that are not captured by state-of-the-art molecular force fields. Although our approach is applied on a set of model systems, it is fully general and may be used to study the conformational dynamics of flexible biomolecules and to detect inaccuracies in molecular dynamics force fields.

Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange.

PubMed

Kubitzki, Marcus B; de Groot, Bert L

2007-06-15

Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of degrees of freedom involved. Aiming at increased sampling efficiency, we present a novel simulation method combining the ideas of essential dynamics and REX. Unlike standard REX, in each replica only a selection of essential collective modes of a subsystem of interest (essential subspace) is coupled to a higher temperature, with the remainder of the system staying at a reference temperature, T(0). This selective excitation along with the replica framework permits efficient approximate ensemble-preserving conformational sampling and allows much larger temperature differences between replicas, thereby considerably enhancing sampling efficiency. Ensemble properties and sampling performance of the method are discussed using dialanine and guanylin test systems, with multi-microsecond molecular dynamics simulations of these test systems serving as references.

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms☆

PubMed Central

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-01-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov. PMID:26766517

Shock-driven fluid-structure interaction for civil design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, Stephen L; Deiterding, Ralf

The multiphysics fluid-structure interaction simulation of shock-loaded structures requires the dynamic coupling of a shock-capturing flow solver to a solid mechanics solver for large deformations. The Virtual Test Facility combines a Cartesian embedded boundary approach with dynamic mesh adaptation in a generic software framework of flow solvers using hydrodynamic finite volume upwind schemes that are coupled to various explicit finite element solid dynamics solvers (Deiterding et al., 2006). This paper gives a brief overview of the computational approach and presents first simulations that utilize the general purpose solid dynamics code DYNA3D for complex 3D structures of interest in civil engineering.more » Results from simulations of a reinforced column, highway bridge, multistory building, and nuclear reactor building are presented.« less

Computational Fluid Dynamics (CFD) Simulation of Hypersonic Turbine-Based Combined-Cycle (TBCC) Inlet Mode Transition

NASA Technical Reports Server (NTRS)

Slater, John W.; Saunders, John D.

2010-01-01

Methods of computational fluid dynamics were applied to simulate the aerodynamics within the turbine flowpath of a turbine-based combined-cycle propulsion system during inlet mode transition at Mach 4. Inlet mode transition involved the rotation of a splitter cowl to close the turbine flowpath to allow the full operation of a parallel dual-mode ramjet/scramjet flowpath. Steady-state simulations were performed at splitter cowl positions of 0deg, -2deg, -4deg, and -5.7deg, at which the turbine flowpath was closed half way. The simulations satisfied one objective of providing a greater understanding of the flow during inlet mode transition. Comparisons of the simulation results with wind-tunnel test data addressed another objective of assessing the applicability of the simulation methods for simulating inlet mode transition. The simulations showed that inlet mode transition could occur in a stable manner and that accurate modeling of the interactions among the shock waves, boundary layers, and porous bleed regions was critical for evaluating the inlet static and total pressures, bleed flow rates, and bleed plenum pressures. The simulations compared well with some of the wind-tunnel data, but uncertainties in both the windtunnel data and simulations prevented a formal evaluation of the accuracy of the simulation methods.

Multiscale modeling of dislocation-precipitate interactions in Fe: From molecular dynamics to discrete dislocations.

PubMed

Lehtinen, Arttu; Granberg, Fredric; Laurson, Lasse; Nordlund, Kai; Alava, Mikko J

2016-01-01

The stress-driven motion of dislocations in crystalline solids, and thus the ensuing plastic deformation process, is greatly influenced by the presence or absence of various pointlike defects such as precipitates or solute atoms. These defects act as obstacles for dislocation motion and hence affect the mechanical properties of the material. Here we combine molecular dynamics studies with three-dimensional discrete dislocation dynamics simulations in order to model the interaction between different kinds of precipitates and a 1/2〈111〉{110} edge dislocation in BCC iron. We have implemented immobile spherical precipitates into the ParaDis discrete dislocation dynamics code, with the dislocations interacting with the precipitates via a Gaussian potential, generating a normal force acting on the dislocation segments. The parameters used in the discrete dislocation dynamics simulations for the precipitate potential, the dislocation mobility, shear modulus, and dislocation core energy are obtained from molecular dynamics simulations. We compare the critical stresses needed to unpin the dislocation from the precipitate in molecular dynamics and discrete dislocation dynamics simulations in order to fit the two methods together and discuss the variety of the relevant pinning and depinning mechanisms.

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations.

PubMed

Kortkhonjia, Ekaterine; Brandman, Relly; Zhou, Joe Zhongxiang; Voelz, Vincent A; Chorny, Ilya; Kabakoff, Bruce; Patapoff, Thomas W; Dill, Ken A; Swartz, Trevor E

2013-01-01

The solution dynamics of antibodies are critical to antibody function. We explore the internal solution dynamics of antibody molecules through the combination of time-resolved fluorescence anisotropy experiments on IgG1 with more than two microseconds of all-atom molecular dynamics (MD) simulations in explicit water, an order of magnitude more than in previous simulations. We analyze the correlated motions with a mutual information entropy quantity, and examine state transition rates in a Markov-state model, to give coarse-grained descriptors of the motions. Our MD simulations show that while there are many strongly correlated motions, antibodies are highly flexible, with F(ab) and F(c) domains constantly forming and breaking contacts, both polar and non-polar. We find that salt bridges break and reform, and not always with the same partners. While the MD simulations in explicit water give the right time scales for the motions, the simulated motions are about 3-fold faster than the experiments. Overall, the picture that emerges is that antibodies do not simply fluctuate around a single state of atomic contacts. Rather, in these large molecules, different atoms come in contact during different motions.

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

NASA Astrophysics Data System (ADS)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Molecular Dynamics of Dense Fluids: Simulation-Theory Symbiosis

NASA Astrophysics Data System (ADS)

Yip, Sidney

35 years ago Berni J. Alder showed the Boltzmann-Enskog kinetic theory failed to adequately account for the viscosity of fluids near solid density as determined by molecular dynamics simulation. This work, along with other notable simulation findings, provided great stimulus to the statistical mechanical studies of transport phenomena, particularly in dealing with collective effects in the time correlation functions of liquids. An extended theoretical challenge that remains partially resolved at best is the shear viscosity of supercooled liquids. How can one give a unified explanation of the so-called fragile and strong characteristic temperature behavior, with implications for the dynamics of glass transition? In this tribute on the occasion of his 90th birthday symposium, we recount a recent study where simulation, combined with heuristic (transition-state) and first principles (linear response) theories, identifies the molecular mechanisms governing glassy-state relaxation. Such an interplay between simulation and theory is progress from the early days; instead of simulation challenging theory, now simulation and theory complement each other.

Dynamic Simulation of a Wave Rotor Topped Turboshaft Engine

NASA Technical Reports Server (NTRS)

Greendyke, R. B.; Paxson, D. E.; Schobeiri, M. T.

1997-01-01

The dynamic behavior of a wave rotor topped turboshaft engine is examined using a numerical simulation. The simulation utilizes an explicit, one-dimensional, multi-passage, CFD based wave rotor code in combination with an implicit, one-dimensional, component level dynamic engine simulation code. Transient responses to rapid fuel flow rate changes and compressor inlet pressure changes are simulated and compared with those of a similarly sized, untopped, turboshaft engine. Results indicate that the wave rotor topped engine responds in a stable, and rapid manner. Furthermore, during certain transient operations, the wave rotor actually tends to enhance engine stability. In particular, there is no tendency toward surge in the compressor of the wave rotor topped engine during rapid acceleration. In fact, the compressor actually moves slightly away from the surge line during this transient. This behavior is precisely the opposite to that of an untopped engine. The simulation is described. Issues associated with integrating CFD and component level codes are discussed. Results from several transient simulations are presented and discussed.

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.

PubMed

Caulfield, Thomas R; Devkota, Batsal; Rollins, Geoffrey C

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

Computational modeling of the effective Young's modulus values of fullerene molecules: a combined molecular dynamics simulation and continuum shell model.

PubMed

Ghavanloo, Esmaeal; Izadi, Razie; Nayebi, Ali

2018-02-28

Estimating the Young's modulus of a structure in the nanometer size range is a difficult task. The reliable determination of this parameter is, however, important in both basic and applied research. In this study, by combining molecular dynamics (MD) simulations and continuum shell theory, we designed a new approach to determining the Young's modulus values of different spherical fullerenes. The results indicate that the Young's modulus values of fullerene molecules decrease nonlinearly with increasing molecule size and understandably tend to the Young's modulus of an ideal flat graphene sheet at large molecular radii. To the best of our knowledge, this is first time that a combined atomistic-continuum method which can predict the Young's modulus values of fullerene molecules with high precision has been reported.

From Particles and Point Clouds to Voxel Models: High Resolution Modeling of Dynamic Landscapes in Open Source GIS

NASA Astrophysics Data System (ADS)

Mitasova, H.; Hardin, E. J.; Kratochvilova, A.; Landa, M.

2012-12-01

Multitemporal data acquired by modern mapping technologies provide unique insights into processes driving land surface dynamics. These high resolution data also offer an opportunity to improve the theoretical foundations and accuracy of process-based simulations of evolving landforms. We discuss development of new generation of visualization and analytics tools for GRASS GIS designed for 3D multitemporal data from repeated lidar surveys and from landscape process simulations. We focus on data and simulation methods that are based on point sampling of continuous fields and lead to representation of evolving surfaces as series of raster map layers or voxel models. For multitemporal lidar data we present workflows that combine open source point cloud processing tools with GRASS GIS and custom python scripts to model and analyze dynamics of coastal topography (Figure 1) and we outline development of coastal analysis toolbox. The simulations focus on particle sampling method for solving continuity equations and its application for geospatial modeling of landscape processes. In addition to water and sediment transport models, already implemented in GIS, the new capabilities under development combine OpenFOAM for wind shear stress simulation with a new module for aeolian sand transport and dune evolution simulations. Comparison of observed dynamics with the results of simulations is supported by a new, integrated 2D and 3D visualization interface that provides highly interactive and intuitive access to the redesigned and enhanced visualization tools. Several case studies will be used to illustrate the presented methods and tools and demonstrate the power of workflows built with FOSS and highlight their interoperability.Figure 1. Isosurfaces representing evolution of shoreline and a z=4.5m contour between the years 1997-2011at Cape Hatteras, NC extracted from a voxel model derived from series of lidar-based DEMs.

High-Performance First-Principles Molecular Dynamics for Predictive Theory and Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gygi, Francois; Galli, Giulia; Schwegler, Eric

This project focused on developing high-performance software tools for First-Principles Molecular Dynamics (FPMD) simulations, and applying them in investigations of materials relevant to energy conversion processes. FPMD is an atomistic simulation method that combines a quantum-mechanical description of electronic structure with the statistical description provided by molecular dynamics (MD) simulations. This reliance on fundamental principles allows FPMD simulations to provide a consistent description of structural, dynamical and electronic properties of a material. This is particularly useful in systems for which reliable empirical models are lacking. FPMD simulations are increasingly used as a predictive tool for applications such as batteries, solarmore » energy conversion, light-emitting devices, electro-chemical energy conversion devices and other materials. During the course of the project, several new features were developed and added to the open-source Qbox FPMD code. The code was further optimized for scalable operation of large-scale, Leadership-Class DOE computers. When combined with Many-Body Perturbation Theory (MBPT) calculations, this infrastructure was used to investigate structural and electronic properties of liquid water, ice, aqueous solutions, nanoparticles and solid-liquid interfaces. Computing both ionic trajectories and electronic structure in a consistent manner enabled the simulation of several spectroscopic properties, such as Raman spectra, infrared spectra, and sum-frequency generation spectra. The accuracy of the approximations used allowed for direct comparisons of results with experimental data such as optical spectra, X-ray and neutron diffraction spectra. The software infrastructure developed in this project, as applied to various investigations of solids, liquids and interfaces, demonstrates that FPMD simulations can provide a detailed, atomic-scale picture of structural, vibrational and electronic properties of complex systems relevant to energy conversion devices.« less

Dynamical scattering in coherent hard x-ray nanobeam Bragg diffraction

NASA Astrophysics Data System (ADS)

Pateras, A.; Park, J.; Ahn, Y.; Tilka, J. A.; Holt, M. V.; Kim, H.; Mawst, L. J.; Evans, P. G.

2018-06-01

Unique intensity features arising from dynamical diffraction arise in coherent x-ray nanobeam diffraction patterns of crystals having thicknesses larger than the x-ray extinction depth or exhibiting combinations of nanoscale and mesoscale features. We demonstrate that dynamical scattering effects can be accurately predicted using an optical model combined with the Darwin theory of dynamical x-ray diffraction. The model includes the highly divergent coherent x-ray nanobeams produced by Fresnel zone plate focusing optics and accounts for primary extinction, multiple scattering, and absorption. The simulation accurately reproduces the dynamical scattering features of experimental diffraction patterns acquired from a GaAs/AlGaAs epitaxial heterostructure on a GaAs (001) substrate.

Quasi-Dynamic Versus Fully-Dynamic Simulations of Slip Accumulation on Faults with Enhanced Dynamic Weakening

NASA Astrophysics Data System (ADS)

Lapusta, N.; Thomas, M.; Noda, H.; Avouac, J.

2012-12-01

Long-term simulations that incorporate both seismic events and aseismic slip are quite important for studies of earthquake physics but challenging computationally. To study long deformation histories, most simulation methods do not incorporate full inertial effects (wave propagation) during simulated earthquakes, using quasi-dynamic approximations instead. Here we compare the results of quasi-dynamic simulations to the fully dynamic ones for a range of problems to determine the applicability of the quasi-dynamic approach. Intuitively, the quasi-dynamic approach should do relatively well in problems where wave-mediated effects are relatively simple but should have substantially different (and hence wrong) response when the wave-mediated stress transfers dominate the character of the seismic events. This is exactly what we observe in our simulations. We consider a 2D model of a rate-and-state fault with a seismogenic (steady-state velocity-weakening) zone surrounded by creeping (steady-state velocity-strengthening) areas. If the seismogenic zone is described by the standard Dieterich-Ruina rate-and-state friction, the resulting earthquake sequences consist of relatively simple crack-like ruptures, and the inclusion of true wave-propagation effects mostly serves to concentrate stress more efficiently at the rupture front. Hence, in such models, rupture speeds and slip rates are significantly (several times) lower in the quasi-dynamic simulations compared to the fully dynamic ones, but the total slip, the crack-like nature of seismic events, and the overall pattern of earthquake sequences is comparable, consistently with prior studies. Such behavior can be classified as qualitatively similar but quantitatively different, and it motivates the popularity of the quasi-dynamic methods in simulations. However, the comparison changes dramatically once we consider a model with enhanced dynamic weakening in the seismogenic zone in the form of flash heating. In this case, the fully dynamic simulations produce seismic ruptures in the form of short-duration slip pulses, where the pulses form due to a combination of enhanced weakening and wave effects. The quasi-dynamic simulations in the same model produce completely different results, with large crack-like ruptures, different total slips, different rupture patterns, and different prestress state before large, model-spanning events. Such qualitative differences between the quasi-dynamic and fully-dynamic simulation should result in any model where inertial effects lead to qualitative differences, such as cases with supershear transition or fault with different materials on the two sides. We will present results on our current work on how the quasi-dynamic and fully dynamic simulations compare for the cases with heterogeneous fault properties.

Composite load spectra for select space propulsion structural components

NASA Technical Reports Server (NTRS)

Newell, J. F.; Kurth, R. E.; Ho, H.

1991-01-01

The objective of this program is to develop generic load models with multiple levels of progressive sophistication to simulate the composite (combined) load spectra that are induced in space propulsion system components, representative of Space Shuttle Main Engines (SSME), such as transfer ducts, turbine blades, and liquid oxygen posts and system ducting. The first approach will consist of using state of the art probabilistic methods to describe the individual loading conditions and combinations of these loading conditions to synthesize the composite load spectra simulation. The second approach will consist of developing coupled models for composite load spectra simulation which combine the deterministic models for composite load dynamic, acoustic, high pressure, and high rotational speed, etc., load simulation using statistically varying coefficients. These coefficients will then be determined using advanced probabilistic simulation methods with and without strategically selected experimental data.

Tackling sampling challenges in biomolecular simulations.

PubMed

Barducci, Alessandro; Pfaendtner, Jim; Bonomi, Massimiliano

2015-01-01

Molecular dynamics (MD) simulations are a powerful tool to give an atomistic insight into the structure and dynamics of proteins. However, the time scales accessible in standard simulations, which often do not match those in which interesting biological processes occur, limit their predictive capabilities. Many advanced sampling techniques have been proposed over the years to overcome this limitation. This chapter focuses on metadynamics, a method based on the introduction of a time-dependent bias potential to accelerate sampling and recover equilibrium properties of a few descriptors that are able to capture the complexity of a process at a coarse-grained level. The theory of metadynamics and its combination with other popular sampling techniques such as the replica exchange method is briefly presented. Practical applications of these techniques to the study of the Trp-Cage miniprotein folding are also illustrated. The examples contain a guide for performing these calculations with PLUMED, a plugin to perform enhanced sampling simulations in combination with many popular MD codes.

Formalizing Knowledge in Multi-Scale Agent-Based Simulations

PubMed Central

Somogyi, Endre; Sluka, James P.; Glazier, James A.

2017-01-01

Multi-scale, agent-based simulations of cellular and tissue biology are increasingly common. These simulations combine and integrate a range of components from different domains. Simulations continuously create, destroy and reorganize constituent elements causing their interactions to dynamically change. For example, the multi-cellular tissue development process coordinates molecular, cellular and tissue scale objects with biochemical, biomechanical, spatial and behavioral processes to form a dynamic network. Different domain specific languages can describe these components in isolation, but cannot describe their interactions. No current programming language is designed to represent in human readable and reusable form the domain specific knowledge contained in these components and interactions. We present a new hybrid programming language paradigm that naturally expresses the complex multi-scale objects and dynamic interactions in a unified way and allows domain knowledge to be captured, searched, formalized, extracted and reused. PMID:29338063

Contact Line Dynamics

NASA Astrophysics Data System (ADS)

Kreiss, Gunilla; Holmgren, Hanna; Kronbichler, Martin; Ge, Anthony; Brant, Luca

2017-11-01

The conventional no-slip boundary condition leads to a non-integrable stress singularity at a moving contact line. This makes numerical simulations of two-phase flow challenging, especially when capillarity of the contact point is essential for the dynamics of the flow. We will describe a modeling methodology, which is suitable for numerical simulations, and present results from numerical computations. The methodology is based on combining a relation between the apparent contact angle and the contact line velocity, with the similarity solution for Stokes flow at a planar interface. The relation between angle and velocity can be determined by theoretical arguments, or from simulations using a more detailed model. In our approach we have used results from phase field simulations in a small domain, but using a molecular dynamics model should also be possible. In both cases more physics is included and the stress singularity is removed.

Formalizing Knowledge in Multi-Scale Agent-Based Simulations.

PubMed

Somogyi, Endre; Sluka, James P; Glazier, James A

2016-10-01

Multi-scale, agent-based simulations of cellular and tissue biology are increasingly common. These simulations combine and integrate a range of components from different domains. Simulations continuously create, destroy and reorganize constituent elements causing their interactions to dynamically change. For example, the multi-cellular tissue development process coordinates molecular, cellular and tissue scale objects with biochemical, biomechanical, spatial and behavioral processes to form a dynamic network. Different domain specific languages can describe these components in isolation, but cannot describe their interactions. No current programming language is designed to represent in human readable and reusable form the domain specific knowledge contained in these components and interactions. We present a new hybrid programming language paradigm that naturally expresses the complex multi-scale objects and dynamic interactions in a unified way and allows domain knowledge to be captured, searched, formalized, extracted and reused.

Using stroboscopic flow imaging to validate large-scale computational fluid dynamics simulations

NASA Astrophysics Data System (ADS)

Laurence, Ted A.; Ly, Sonny; Fong, Erika; Shusteff, Maxim; Randles, Amanda; Gounley, John; Draeger, Erik

2017-02-01

The utility and accuracy of computational modeling often requires direct validation against experimental measurements. The work presented here is motivated by taking a combined experimental and computational approach to determine the ability of large-scale computational fluid dynamics (CFD) simulations to understand and predict the dynamics of circulating tumor cells in clinically relevant environments. We use stroboscopic light sheet fluorescence imaging to track the paths and measure the velocities of fluorescent microspheres throughout a human aorta model. Performed over complex physiologicallyrealistic 3D geometries, large data sets are acquired with microscopic resolution over macroscopic distances.

Combined state and parameter identification of nonlinear structural dynamical systems based on Rao-Blackwellization and Markov chain Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Abhinav, S.; Manohar, C. S.

2018-03-01

The problem of combined state and parameter estimation in nonlinear state space models, based on Bayesian filtering methods, is considered. A novel approach, which combines Rao-Blackwellized particle filters for state estimation with Markov chain Monte Carlo (MCMC) simulations for parameter identification, is proposed. In order to ensure successful performance of the MCMC samplers, in situations involving large amount of dynamic measurement data and (or) low measurement noise, the study employs a modified measurement model combined with an importance sampling based correction. The parameters of the process noise covariance matrix are also included as quantities to be identified. The study employs the Rao-Blackwellization step at two stages: one, associated with the state estimation problem in the particle filtering step, and, secondly, in the evaluation of the ratio of likelihoods in the MCMC run. The satisfactory performance of the proposed method is illustrated on three dynamical systems: (a) a computational model of a nonlinear beam-moving oscillator system, (b) a laboratory scale beam traversed by a loaded trolley, and (c) an earthquake shake table study on a bending-torsion coupled nonlinear frame subjected to uniaxial support motion.

Use of simulated satellite radiances from a mesoscale numerical model to understand kinematic and dynamic processes

NASA Technical Reports Server (NTRS)

Kalb, Michael; Robertson, Franklin; Jedlovec, Gary; Perkey, Donald

1987-01-01

Techniques by which mesoscale numerical weather prediction model output and radiative transfer codes are combined to simulate the radiance fields that a given passive temperature/moisture satellite sensor would see if viewing the evolving model atmosphere are introduced. The goals are to diagnose the dynamical atmospheric processes responsible for recurring patterns in observed satellite radiance fields, and to develop techniques to anticipate the ability of satellite sensor systems to depict atmospheric structures and provide information useful for numerical weather prediction (NWP). The concept of linking radiative transfer and dynamical NWP codes is demonstrated with time sequences of simulated radiance imagery in the 24 TIROS vertical sounder channels derived from model integrations for March 6, 1982.

Faster protein folding using enhanced conformational sampling of molecular dynamics simulation.

PubMed

Kamberaj, Hiqmet

2018-05-01

In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method. In addition, we applied SPMD simulation to calculate the time correlation functions of the transitions in a two dimensional surface to demonstrate the enhancement of transition path sampling. Our results showed that folded structure can be obtained in a shorter simulation time using the new method when compared with non-augmented dynamical system. Typically, in less than 0.5 ns using replica exchange runs assuming that native folded structure is known and within simulation time scale of 40 ns in the case of blind structure prediction. Furthermore, the root mean square deviations from the reference structures were less than 2Å. To demonstrate the performance of new method, we also implemented three simulation protocols using CHARMM software. Comparisons are also performed with standard targeted molecular dynamics simulation method. Copyright © 2018 Elsevier Inc. All rights reserved.

Combined aerodynamic and structural dynamic problem emulating routines (CASPER): Theory and implementation

NASA Technical Reports Server (NTRS)

Jones, William H.

1985-01-01

The Combined Aerodynamic and Structural Dynamic Problem Emulating Routines (CASPER) is a collection of data-base modification computer routines that can be used to simulate Navier-Stokes flow through realistic, time-varying internal flow fields. The Navier-Stokes equation used involves calculations in all three dimensions and retains all viscous terms. The only term neglected in the current implementation is gravitation. The solution approach is of an interative, time-marching nature. Calculations are based on Lagrangian aerodynamic elements (aeroelements). It is assumed that the relationships between a particular aeroelement and its five nearest neighbor aeroelements are sufficient to make a valid simulation of Navier-Stokes flow on a small scale and that the collection of all small-scale simulations makes a valid simulation of a large-scale flow. In keeping with these assumptions, it must be noted that CASPER produces an imitation or simulation of Navier-Stokes flow rather than a strict numerical solution of the Navier-Stokes equation. CASPER is written to operate under the Parallel, Asynchronous Executive (PAX), which is described in a separate report.

On-the-fly transition search and applications to temperature-accelerated dynamics

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Amar, Jacques

2015-03-01

Temperature-accelerated dynamics (TAD) is a powerful method to study non-equilibrium processes and has been providing surprising insights for a variety of systems. While serial TAD simulations have been limited by the roughly N3 increase in the computational cost as a function of the number of atoms N in the system, recently we have shown that by carrying out parallel TAD simulations which combine spatial decomposition with our semi-rigorous synchronous sublattice algorithm, significantly improved scaling is possible. However, in this approach the size of activated events is limited by the processor size while the dynamics is not exact. Here we discuss progress in improving the scaling of serial TAD by combining the use of on-the-fly transition searching with our previously developed localized saddle-point method. We demonstrate improved performance for the cases of Ag/Ag(100) annealing and Cu/Cu(100) growth. Supported by NSF DMR-1410840.

The Simulation of Vibrations of Railway Beam Bridges in the Object-oriented Environment Delphi

NASA Astrophysics Data System (ADS)

Raspopov, Alexander; Artyomov, Vitaly; Rusu, Sergey

2010-01-01

The peculiarities of combination of finite-element method and equations of solid dynamics, the basic stages of development of the program complex Belinda for calculation of statics and dynamics of the rods constructions as applied to railway bridges are described.

Combining experimental and simulation data of molecular processes via augmented Markov models.

PubMed

Olsson, Simon; Wu, Hao; Paul, Fabian; Clementi, Cecilia; Noé, Frank

2017-08-01

Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few [Formula: see text], which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.

Combining configurational energies and forces for molecular force field optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Combining configurational energies and forces for molecular force field optimization

DOE PAGES

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

2017-07-21

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Love-Wave Sensors Combined with Microfluidics for Fast Detection of Biological Warfare Agents

PubMed Central

Matatagui, Daniel; Fontecha, José Luis; Fernández, María Jesús; Gràcia, Isabel; Cané, Carles; Santos, José Pedro; Horrillo, María Carmen

2014-01-01

The following paper examines a time-efficient method for detecting biological warfare agents (BWAs). The method is based on a system of a Love-wave immunosensor combined with a microfluidic chip which detects BWA samples in a dynamic mode. In this way a continuous flow-through of the sample is created, promoting the reaction between antigen and antibody and allowing a fast detection of the BWAs. In order to prove this method, static and dynamic modes have been simulated and different concentrations of BWA simulants have been tested with two immunoreactions: phage M13 has been detected using the mouse monoclonal antibody anti-M13 (AM13), and the rabbit immunoglobulin (Rabbit IgG) has been detected using the polyclonal antibody goat anti-rabbit (GAR). Finally, different concentrations of each BWA simulants have been detected with a fast response time and a desirable level of discrimination among them has been achieved. PMID:25029282

Multibody dynamic simulation of knee contact mechanics

PubMed Central

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

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

PubMed

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Relaxation dynamics of internal segments of DNA chains in nanochannels

NASA Astrophysics Data System (ADS)

Jain, Aashish; Muralidhar, Abhiram; Dorfman, Kevin; Dorfman Group Team

We will present relaxation dynamics of internal segments of a DNA chain confined in nanochannel. The results have direct application in genome mapping technology, where long DNA molecules containing sequence-specific fluorescent probes are passed through an array of nanochannels to linearize them, and then the distances between these probes (the so-called ``DNA barcode'') are measured. The relaxation dynamics of internal segments set the experimental error due to dynamic fluctuations. We developed a multi-scale simulation algorithm, combining a Pruned-Enriched Rosenbluth Method (PERM) simulation of a discrete wormlike chain model with hard spheres with Brownian dynamics (BD) simulations of a bead-spring chain. Realistic parameters such as the bead friction coefficient and spring force law parameters are obtained from PERM simulations and then mapped onto the bead-spring model. The BD simulations are carried out to obtain the extension autocorrelation functions of various segments, which furnish their relaxation times. Interestingly, we find that (i) corner segments relax faster than the center segments and (ii) relaxation times of corner segments do not depend on the contour length of DNA chain, whereas the relaxation times of center segments increase linearly with DNA chain size.

Reaching extended length-scales with temperature-accelerated dynamics

NASA Astrophysics Data System (ADS)

Amar, Jacques G.; Shim, Yunsic

2013-03-01

In temperature-accelerated dynamics (TAD) a high-temperature molecular dynamics (MD) simulation is used to accelerate the search for the next low-temperature activated event. While TAD has been quite successful in extending the time-scales of simulations of non-equilibrium processes, due to the fact that the computational work scales approximately as the cube of the number of atoms, until recently only simulations of relatively small systems have been carried out. Recently, we have shown that by combining spatial decomposition with our synchronous sublattice algorithm, significantly improved scaling is possible. However, in this approach the size of activated events is limited by the processor size while the dynamics is not exact. Here we discuss progress in developing an alternate approach in which high-temperature parallel MD along with localized saddle-point (LSAD) calculations, are used to carry out TAD simulations without restricting the size of activated events while keeping the dynamics ``exact'' within the context of harmonic transition-state theory. In tests of our LSAD method applied to Ag/Ag(100) annealing and Cu/Cu(100) growth simulations we find significantly improved scaling of TAD, while maintaining a negligibly small error in the energy barriers. Supported by NSF DMR-0907399.

Theoretical Chemistry Comes Alive: Full Partner with Experiment.

ERIC Educational Resources Information Center

Goddard, William A., III

1985-01-01

The expected thrust for theoretical chemistry in the next decade will be to combine knowledge of fundamental chemical steps/interactions with advances in chemical dynamics, irreversible statistical mechanics, and computer technology to produce simulations of chemical systems with reaction site competition. A sample simulation (using the enzyme…

Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong; Plankensteiner, Kristof; Rode, Bernd M

2004-10-01

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value. Copyright 2004 Wiley Periodicals, Inc.

Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.

PubMed

Zanchi, Fernando Berton; Caceres, Rafael Andrade; Stabeli, Rodrigo Guerino; de Azevedo, Walter Filgueira

2010-03-01

Purine nucleoside phosphorylase (PNP) (EC.2.4.2.1) is an enzyme that catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is involved in purine-salvage pathway and has been proposed as a promising target for design and development of antimalarial and antibacterial drugs. Recent elucidation of the three-dimensional structure of PNP by X-ray protein crystallography left open the possibility of structure-based virtual screening initiatives in combination with molecular dynamics simulations focused on identification of potential new antimalarial drugs. Most of the previously published molecular dynamics simulations of PNP were carried out on human PNP, a trimeric PNP. The present article describes for the first time molecular dynamics simulations of hexameric PNP from Plasmodium falciparum (PfPNP). Two systems were simulated in the present work, PfPNP in ligand free form, and in complex with immucillin and sulfate. Based on the dynamical behavior of both systems the main results related to structural stability and protein-drug interactions are discussed.

A hybrid algorithm for parallel molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Mangiardi, Chris M.; Meyer, R.

2017-10-01

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

PubMed

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-07-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Density functional theory calculation of refractive indices of liquid-forming silicon oil compounds

NASA Astrophysics Data System (ADS)

Lee, Sanghun; Park, Sung Soo; Hagelberg, Frank

2012-02-01

A combination of quantum chemical calculation and molecular dynamics simulation is applied to compute refractive indices of liquid-forming silicon oils. The densities of these species are obtained from molecular dynamics simulations based on the NPT ensemble while the molecular polarizabilities are evaluated by density functional theory. This procedure is shown to yield results well compatible with available experimental data, suggesting that it represents a robust and economic route for determining the refractive indices of liquid-forming organic complexes containing silicon.

Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

PubMed Central

2016-01-01

Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757

Guided self-assembly of magnetic beads for biomedical applications

NASA Astrophysics Data System (ADS)

Gusenbauer, Markus; Nguyen, Ha; Reichel, Franz; Exl, Lukas; Bance, Simon; Fischbacher, Johann; Özelt, Harald; Kovacs, Alexander; Brandl, Martin; Schrefl, Thomas

2014-02-01

Micromagnetic beads are widely used in biomedical applications for cell separation, drug delivery, and hyperthermia cancer treatment. Here we propose to use self-organized magnetic bead structures which accumulate on fixed magnetic seeding points to isolate circulating tumor cells. The analysis of circulating tumor cells is an emerging tool for cancer biology research and clinical cancer management including the detection, diagnosis and monitoring of cancer. Microfluidic chips for isolating circulating tumor cells use either affinity, size or density capturing methods. We combine multiphysics simulation techniques to understand the microscopic behavior of magnetic beads interacting with soft magnetic accumulation points used in lab-on-chip technologies. Our proposed chip technology offers the possibility to combine affinity and size capturing with special antibody-coated bead arrangements using a magnetic gradient field created by Neodymium Iron Boron permanent magnets. The multiscale simulation environment combines magnetic field computation, fluid dynamics and discrete particle dynamics.

Simulating Effects of High Angle of Attack on Turbofan Engine Performance

NASA Technical Reports Server (NTRS)

Liu, Yuan; Claus, Russell W.; Litt, Jonathan S.; Guo, Ten-Huei

2013-01-01

A method of investigating the effects of high angle of attack (AOA) flight on turbofan engine performance is presented. The methodology involves combining a suite of diverse simulation tools. Three-dimensional, steady-state computational fluid dynamics (CFD) software is used to model the change in performance of a commercial aircraft-type inlet and fan geometry due to various levels of AOA. Parallel compressor theory is then applied to assimilate the CFD data with a zero-dimensional, nonlinear, dynamic turbofan engine model. The combined model shows that high AOA operation degrades fan performance and, thus, negatively impacts compressor stability margins and engine thrust. In addition, the engine response to high AOA conditions is shown to be highly dependent upon the type of control system employed.

Multicanonical molecular dynamics simulations combined with Metadynamics for the free energy landscape of a biomolecular system with high energy barriers

NASA Astrophysics Data System (ADS)

Yonezawa, Yasushige; Shimoyama, Hiromitsu; Nakamura, Haruki

2011-01-01

Multicanonical molecular-dynamics (McMD) simulation and Metadynamics (MetaD) are useful for obtaining the free-energies, and can be mutually complementary. We combined McMD with MetaD, and applied it to the conformational free energy calculations of a proline dipeptide. First, MetaD was performed along the dihedral angle at the prolyl bond and we obtained a coarse biasing potential. After adding the biasing potential to the dihedral angle potential energy, we conducted McMD with the modified potential energy. Enhanced sampling was achieved for all degrees-of-freedom, and the sampling of the dihedral angle space was facilitated. After reweighting, we obtained an accurate free energy landscape.

SAINT: A combined simulation language for modeling man-machine systems

NASA Technical Reports Server (NTRS)

Seifert, D. J.

1979-01-01

SAINT (Systems Analysis of Integrated Networks of Tasks) is a network modeling and simulation technique for design and analysis of complex man machine systems. SAINT provides the conceptual framework for representing systems that consist of discrete task elements, continuous state variables, and interactions between them. It also provides a mechanism for combining human performance models and dynamic system behaviors in a single modeling structure. The SAINT technique is described and applications of the SAINT are discussed.

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

NASA Astrophysics Data System (ADS)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Dynamic Stall Patterns

NASA Astrophysics Data System (ADS)

Davidson, Phillip; Babbitt, Ashli; Magstadt, Andrew; Nikoueeyan, Pourya; Naughton, Jonathan; Jonathan Naughton Team

2014-11-01

The performance of helicopter and wind turbine blades is affected by dynamic stall. Dynamic stall has received considerable attention, but it is still difficult to simulate and not fully understood. Over the past seven years, many airfoils for helicopter and wind turbine use ranging from 9.5 to 30% thick have been experimentally tested and simulated while dynamically pitching to further characterize dynamic stall. Tests have been run at chord Reynolds number between 225,000-440,000 for various reduced frequencies, mean angles of attack, and oscillation amplitudes. Characterization of stall has been accomplished using data from previous studies as well as the unsteady pressure and flow-field data available from our own work. Where available, combined surface and flow-field data allow for clear identification of the types of stall observed and the flow structure associated with them. The results indicate that thin airfoil stall, leading edge stall, and trailing edge stall are observed in the oscillating airfoil experiments and simulations. These three main stall types are further divided into subcategories. By improving our understanding of the features of dynamic stall, it is expected that physics-based simulations can be improved. Work supported by DOE and a gift from BP.

Bivalves: From individual to population modelling

NASA Astrophysics Data System (ADS)

Saraiva, S.; van der Meer, J.; Kooijman, S. A. L. M.; Ruardij, P.

2014-11-01

An individual based population model for bivalves was designed, built and tested in a 0D approach, to simulate the population dynamics of a mussel bed located in an intertidal area. The processes at the individual level were simulated following the dynamic energy budget theory, whereas initial egg mortality, background mortality, food competition, and predation (including cannibalism) were additional population processes. Model properties were studied through the analysis of theoretical scenarios and by simulation of different mortality parameter combinations in a realistic setup, imposing environmental measurements. Realistic criteria were applied to narrow down the possible combination of parameter values. Field observations obtained in the long-term and multi-station monitoring program were compared with the model scenarios. The realistically selected modeling scenarios were able to reproduce reasonably the timing of some peaks in the individual abundances in the mussel bed and its size distribution but the number of individuals was not well predicted. The results suggest that the mortality in the early life stages (egg and larvae) plays an important role in population dynamics, either by initial egg mortality, larvae dispersion, settlement failure or shrimp predation. Future steps include the coupling of the population model with a hydrodynamic and biogeochemical model to improve the simulation of egg/larvae dispersion, settlement probability, food transport and also to simulate the feedback of the organisms' activity on the water column properties, which will result in an improvement of the food quantity and quality characterization.

Improved global simulation of groundwater-ecosystem interactions via tight coupling of a dynamic global ecosystem model and a global hydrological model

NASA Astrophysics Data System (ADS)

Braakhekke, Maarten; Rebel, Karin; Dekker, Stefan; Smith, Benjamin; Sutanudjaja, Edwin; van Beek, Rens; van Kampenhout, Leo; Wassen, Martin

2017-04-01

In up to 30% of the global land surface ecosystems are potentially influenced by the presence of a shallow groundwater table. In these regions upward water flux by capillary rise increases soil moisture availability in the root zone, which has a strong effect on evapotranspiration, vegetation dynamics, and fluxes of carbon and nitrogen. Most global hydrological models and several land surface models simulate groundwater table dynamics and their effects on land surface processes. However, these models typically have relatively simplistic representation of vegetation and do not consider changes in vegetation type and structure. Dynamic global vegetation models (DGVMs), describe land surface from an ecological perspective, combining detailed description of vegetation dynamics and structure, and biogeochemical processes and are thus more appropriate to simulate the ecological and biogeochemical effects of groundwater interactions. However, currently virtually all DGVMs ignore these effects, assuming that water tables are too deep to affect soil moisture in the root zone. We have implemented a tight coupling between the dynamic global ecosystem model LPJ-GUESS and the global hydrological model PCR-GLOBWB, which explicitly simulates groundwater dynamics. This coupled model allows us to explicitly account for groundwater effects on terrestrial ecosystem processes at global scale. Results of global simulations indicate that groundwater strongly influences fluxes of water, carbon and nitrogen, in many regions, adding up to a considerable effect at the global scale.

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

PubMed Central

Caulfield, Thomas R.; Devkota, Batsal; Rollins, Geoffrey C.

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16. PMID:21716650

High Performance Parallel Processing (HPPP) Finite Element Simulation of Fluid Structure Interactions Final Report CRADA No. TC-0824-94-A

DOE Office of Scientific and Technical Information (OSTI.GOV)

Couch, R.; Ziegler, D. P.

This project was a muki-partner CRADA. This was a partnership between Alcoa and LLNL. AIcoa developed a system of numerical simulation modules that provided accurate and efficient threedimensional modeling of combined fluid dynamics and structural response.

Distribution and Dynamic Properties of Xenon Dissolved in the Ionic Smectic Phase of [C16mim][NO3]: MD Simulation and Theoretical Model.

PubMed

Frezzato, Diego; Saielli, Giacomo

2016-03-10

We have investigated the structural and dynamic properties of Xe dissolved in the ionic liquid crystal (ILC) phase of 1-hexadecyl-3-methylimidazolium nitrate using classical molecular dynamics (MD) simulations. Xe is found to be preferentially dissolved within the hydrophobic environment of the alkyl chains rather than in the ionic layers of the smectic phase. The structural parameters and the estimated local diffusion coefficients concerning the short-time motion of Xe are used to parametrize a theoretical model based on the Smoluchowski equation for the macroscopic dynamics across the smectic layers, a feature which cannot be directly obtained from the relatively short MD simulations. This protocol represents an efficient combination of computational and theoretical tools to obtain information on slow processes concerning the permeability and diffusivity of the xenon in smectic ILCs.

Structure and dynamics of acetate anion-based ionic liquids from molecular dynamics study

NASA Astrophysics Data System (ADS)

Chandran, Aneesh; Prakash, Karthigeyan; Senapati, Sanjib

2010-08-01

Acetate anion-based ionic liquids (ILs) have found wide range of applications. The microstructure and dynamics of this IL family have not been clearly understood yet. We report molecular dynamics simulation results of three acetate anion-based ionic liquids that encompass the most common IL cations. Simulations are performed based on a set of proposed force field parameters for IL acetate anion which can be combined with existing parameters for IL cations to simulate large variety of ILs. The computed liquid density and IR spectral data for [BMIM][Ac] are found to match very well with available experimental results. The strong amino-group-associated interactions in [TMG][Ac] are seen to bring about higher cohesive energy density, stronger ion packing, and more restricted translational and rotational mobilities of the constituent ions. The IL anions are found to track the cation movements in all systems, implying that ions in ILs travel in pairs or clusters.

A Simulation Environment for the Dynamic Evaluation of Disaster Preparedness Policies and Interventions

PubMed Central

Lewis, Bryan; Swarup, Samarth; Bisset, Keith; Eubank, Stephen; Marathe, Madhav; Barrett, Chris

2013-01-01

Disasters affect a society at many levels. Simulation based studies often evaluate the effectiveness of one or two response policies in isolation and are unable to represent impact of the policies to coevolve with others. Similarly, most in-depth analyses are based on a static assessment of the “aftermath” rather than capturing dynamics. We have developed a data-centric simulation environment for applying a systems approach to a dynamic analysis of complex combinations of disaster responses. We analyze an improvised nuclear detonation in Washington DC with this environment. The simulated blast affects the transportation system, communications infrastructure, electrical power system, behaviors and motivations of population, and health status of survivors. The effectiveness of partially restoring wireless communications capacity is analyzed in concert with a range of other disaster response policies. Despite providing a limited increase in cell phone communication, overall health was improved. PMID:23903394

Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling.

PubMed

Martins-Costa, Marilia T C; Ruiz-López, Manuel F

2017-04-15

We report an enhanced sampling technique that allows to reach the multi-nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid-vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall-clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.

PubMed

Decherchi, Sergio; Berteotti, Anna; Bottegoni, Giovanni; Rocchia, Walter; Cavalli, Andrea

2015-01-27

The study of biomolecular interactions between a drug and its biological target is of paramount importance for the design of novel bioactive compounds. In this paper, we report on the use of molecular dynamics (MD) simulations and machine learning to study the binding mechanism of a transition state analogue (DADMe-immucillin-H) to the purine nucleoside phosphorylase (PNP) enzyme. Microsecond-long MD simulations allow us to observe several binding events, following different dynamical routes and reaching diverse binding configurations. These simulations are used to estimate kinetic and thermodynamic quantities, such as kon and binding free energy, obtaining a good agreement with available experimental data. In addition, we advance a hypothesis for the slow-onset inhibition mechanism of DADMe-immucillin-H against PNP. Combining extensive MD simulations with machine learning algorithms could therefore be a fruitful approach for capturing key aspects of drug-target recognition and binding.

Towards developing a compact model for magnetization switching in straintronics magnetic random access memory devices

NASA Astrophysics Data System (ADS)

Barangi, Mahmood; Erementchouk, Mikhail; Mazumder, Pinaki

2016-08-01

Strain-mediated magnetization switching in a magnetic tunneling junction (MTJ) by exploiting a combination of piezoelectricity and magnetostriction has been proposed as an energy efficient alternative to spin transfer torque (STT) and field induced magnetization switching methods in MTJ-based magnetic random access memories (MRAM). Theoretical studies have shown the inherent advantages of strain-assisted switching, and the dynamic response of the magnetization has been modeled using the Landau-Lifshitz-Gilbert (LLG) equation. However, an attempt to use LLG for simulating dynamics of individual elements in large-scale simulations of multi-megabyte straintronics MRAM leads to extremely time-consuming calculations. Hence, a compact analytical solution, predicting the flipping delay of the magnetization vector in the nanomagnet under stress, combined with a liberal approximation of the LLG dynamics in the straintronics MTJ, can lead to a simplified model of the device suited for fast large-scale simulations of multi-megabyte straintronics MRAMs. In this work, a tensor-based approach is developed to study the dynamic behavior of the stressed nanomagnet. First, using the developed method, the effect of stress on the switching behavior of the magnetization is investigated to realize the margins between the underdamped and overdamped regimes. The latter helps the designer realize the oscillatory behavior of the magnetization when settling along the minor axis, and the dependency of oscillations on the stress level and the damping factor. Next, a theoretical model to predict the flipping delay of the magnetization vector is developed and tested against LLG-based numerical simulations to confirm the accuracy of findings. Lastly, the obtained delay is incorporated into the approximate solutions of the LLG dynamics, in order to create a compact model to liberally and quickly simulate the magnetization dynamics of the MTJ under stress. Using the developed delay equation, the efficiency of the straintronics switching over the STT method is highlighted by analytically investigating the energy-delay trade-off of both methodologies.

Towards developing a compact model for magnetization switching in straintronics magnetic random access memory devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barangi, Mahmood, E-mail: barangi@umich.edu; Erementchouk, Mikhail; Mazumder, Pinaki

Strain-mediated magnetization switching in a magnetic tunneling junction (MTJ) by exploiting a combination of piezoelectricity and magnetostriction has been proposed as an energy efficient alternative to spin transfer torque (STT) and field induced magnetization switching methods in MTJ-based magnetic random access memories (MRAM). Theoretical studies have shown the inherent advantages of strain-assisted switching, and the dynamic response of the magnetization has been modeled using the Landau-Lifshitz-Gilbert (LLG) equation. However, an attempt to use LLG for simulating dynamics of individual elements in large-scale simulations of multi-megabyte straintronics MRAM leads to extremely time-consuming calculations. Hence, a compact analytical solution, predicting the flippingmore » delay of the magnetization vector in the nanomagnet under stress, combined with a liberal approximation of the LLG dynamics in the straintronics MTJ, can lead to a simplified model of the device suited for fast large-scale simulations of multi-megabyte straintronics MRAMs. In this work, a tensor-based approach is developed to study the dynamic behavior of the stressed nanomagnet. First, using the developed method, the effect of stress on the switching behavior of the magnetization is investigated to realize the margins between the underdamped and overdamped regimes. The latter helps the designer realize the oscillatory behavior of the magnetization when settling along the minor axis, and the dependency of oscillations on the stress level and the damping factor. Next, a theoretical model to predict the flipping delay of the magnetization vector is developed and tested against LLG-based numerical simulations to confirm the accuracy of findings. Lastly, the obtained delay is incorporated into the approximate solutions of the LLG dynamics, in order to create a compact model to liberally and quickly simulate the magnetization dynamics of the MTJ under stress. Using the developed delay equation, the efficiency of the straintronics switching over the STT method is highlighted by analytically investigating the energy-delay trade-off of both methodologies.« less

Classical-trajectory simulation of accelerating neutral atoms with polarized intense laser pulses

NASA Astrophysics Data System (ADS)

Xia, Q. Z.; Fu, L. B.; Liu, J.

2013-03-01

In the present paper, we perform the classical trajectory Monte Carlo simulation of the complex dynamics of accelerating neutral atoms with linearly or circularly polarized intense laser pulses. Our simulations involve the ion motion as well as the tunneling ionization and the scattering dynamics of valence electron in the combined Coulomb and electromagnetic fields, for both helium (He) and magnesium (Mg). We show that for He atoms, only linearly polarized lasers can effectively accelerate the atoms, while for Mg atoms, we find that both linearly and circularly polarized lasers can successively accelerate the atoms. The underlying mechanism is discussed and the subcycle dynamics of accelerating trajectories is investigated. We have compared our theoretical results with a recent experiment [Eichmann Nature (London)NATUAS0028-083610.1038/nature08481 461, 1261 (2009)].

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning

PubMed Central

Matsunaga, Yasuhiro

2018-01-01

Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. The former provide time-series data, such as donor-acceptor distances, whereas the latter give atomistic information, although this information is often biased by model parameters. Here, we devise a machine-learning method to combine the complementary information from the two approaches and construct a consistent model of conformational dynamics. It is applied to the folding dynamics of the formin-binding protein WW domain. MD simulations over 400 μs led to an initial Markov state model (MSM), which was then "refined" using single-molecule Förster resonance energy transfer (FRET) data through hidden Markov modeling. The refined or data-assimilated MSM reproduces the FRET data and features hairpin one in the transition-state ensemble, consistent with mutation experiments. The folding pathway in the data-assimilated MSM suggests interplay between hydrophobic contacts and turn formation. Our method provides a general framework for investigating conformational transitions in other proteins. PMID:29723137

Unraveling the Dynamics of Aminopolymer/Silica Composites

DOE PAGES

Carrillo, Jan-Michael Y.; Sakwa-Novak, Miles A.; Holewinski, Adam; ...

2016-02-25

Branched poly(ethylenimine) (PEI) encapsulated within mesoporous silica (SBA-15), has proven to be an eective sorbent for developing carbon capture technologies. However, the structure-property correlations which govern their adsorptive properties is not well understood. By combining coarse-grained molecular dynamics simulations and neutron scattering experiments we are able to construct, and validate, a detailed model of the dynamics and morphology of the conned polymer within the mesoporous support. By varying the simulation properties we are able to probe, for the rst time, the direct relationship between the structure of the polymer and the non-monotonic dynamics of the polymer as a function ofmore » monomer concentration within an adsorbing cylindrical pore. Overall the simulation results are in good agreement with quasi-elastic neutron scattering (QENS) studies, suggesting an approach that can be a useful guide for understanding how to tune porous polymer composites for enhancing desired dynamical and structural behavior targeting enhanced carbon dioxide adsorption.« less

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning.

PubMed

Matsunaga, Yasuhiro; Sugita, Yuji

2018-05-03

Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. The former provide time-series data, such as donor-acceptor distances, whereas the latter give atomistic information, although this information is often biased by model parameters. Here, we devise a machine-learning method to combine the complementary information from the two approaches and construct a consistent model of conformational dynamics. It is applied to the folding dynamics of the formin-binding protein WW domain. MD simulations over 400 μs led to an initial Markov state model (MSM), which was then "refined" using single-molecule Förster resonance energy transfer (FRET) data through hidden Markov modeling. The refined or data-assimilated MSM reproduces the FRET data and features hairpin one in the transition-state ensemble, consistent with mutation experiments. The folding pathway in the data-assimilated MSM suggests interplay between hydrophobic contacts and turn formation. Our method provides a general framework for investigating conformational transitions in other proteins. © 2018, Matsunaga et al.

Importance of Vibronic Effects in the UV-Vis Spectrum of the 7,7,8,8-Tetracyanoquinodimethane Anion.

PubMed

Tapavicza, Enrico; Furche, Filipp; Sundholm, Dage

2016-10-11

We present a computational method for simulating vibronic absorption spectra in the ultraviolet-visible (UV-vis) range and apply it to the 7,7,8,8-tetracyanoquinodimethane anion (TCNQ - ), which has been used as a ligand in black absorbers. Gaussian broadening of vertical electronic excitation energies of TCNQ - from linear-response time-dependent density functional theory produces only one band, which is qualitatively incorrect. Thus, the harmonic vibrational modes of the two lowest doublet states were computed, and the vibronic UV-vis spectrum was simulated using the displaced harmonic oscillator approximation, the frequency-shifted harmonic oscillator approximation, and the full Duschinsky formalism. An efficient real-time generating function method was implemented to avoid the exponential complexity of conventional Franck-Condon approaches to vibronic spectra. The obtained UV-vis spectra for TCNQ - agree well with experiment; the Duschinsky rotation is found to have only a minor effect on the spectrum. Born-Oppenheimer molecular dynamics simulations combined with calculations of the electronic excitation energies for a large number of molecular structures were also used for simulating the UV-vis spectrum. The Born-Oppenheimer molecular dynamics simulations yield a broadening of the energetically lowest peak in the absorption spectrum, but additional vibrational bands present in the experimental and simulated quantum harmonic oscillator spectra are not observed in the molecular dynamics simulations. Our results underline the importance of vibronic effects for the UV-vis spectrum of TCNQ - , and they establish an efficient method for obtaining vibronic spectra using a combination of linear-response time-dependent density functional theory and a real-time generating function approach.

Accounting for system dynamics in reserve design.

PubMed

Leroux, Shawn J; Schmiegelow, Fiona K A; Cumming, Steve G; Lessard, Robert B; Nagy, John

2007-10-01

Systematic conservation plans have only recently considered the dynamic nature of ecosystems. Methods have been developed to incorporate climate change, population dynamics, and uncertainty in reserve design, but few studies have examined how to account for natural disturbance. Considering natural disturbance in reserve design may be especially important for the world's remaining intact areas, which still experience active natural disturbance regimes. We developed a spatially explicit, dynamic simulation model, CONSERV, which simulates patch dynamics and fire, and used it to evaluate the efficacy of hypothetical reserve networks in northern Canada. We designed six networks based on conventional reserve design methods, with different conservation targets for woodland caribou habitat, high-quality wetlands, vegetation, water bodies, and relative connectedness. We input the six reserve networks into CONSERV and tracked the ability of each to maintain initial conservation targets through time under an active natural disturbance regime. None of the reserve networks maintained all initial targets, and some over-represented certain features, suggesting that both effectiveness and efficiency of reserve design could be improved through use of spatially explicit dynamic simulation during the planning process. Spatial simulation models of landscape dynamics are commonly used in natural resource management, but we provide the first illustration of their potential use for reserve design. Spatial simulation models could be used iteratively to evaluate competing reserve designs and select targets that have a higher likelihood of being maintained through time. Such models could be combined with dynamic planning techniques to develop a general theory for reserve design in an uncertain world.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System T-MATS

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

Molecular Simulations of The Formation of Gold-Molecule-Gold Junctions

NASA Astrophysics Data System (ADS)

Wang, Huachuan

2013-03-01

We perform classical molecular simulations by combining grand canonical Monte Carlo (GCMC) sampling with molecular dynamics (MD) simulation to explore the dynamic gold nanojunctions in a Alkenedithiol (ADT) solvent. With the aid of a simple driving-spring model, which can reasonably represent the long-range elasticity of the gold electrode, the spring forces are obtained during the dynamic stretching procedure. A specific multi-time-scale double reversible reference system propagator (double-RESPA) algorithm has been designed for the metal-organic complex in MD simulations to identify the detailed metal-molecule bonding geometry at metal-molecule-metal interface. We investigate the variations of bonding sites of ADT molecules on gold nanojunctions at Au (111) surface at a constant chemical potential. Simulation results show that an Au-ADT-Au interface is formed on Au nanojunctions, bond-breaking intersection is at 1-1 bond of the monatomic chain of the cross-section, instead of at the Au-S bond. Breaking force is around 1.5 nN. These are consistent with the experimental measurements.

Simulations for designing and interpreting intervention trials in infectious diseases.

PubMed

Halloran, M Elizabeth; Auranen, Kari; Baird, Sarah; Basta, Nicole E; Bellan, Steven E; Brookmeyer, Ron; Cooper, Ben S; DeGruttola, Victor; Hughes, James P; Lessler, Justin; Lofgren, Eric T; Longini, Ira M; Onnela, Jukka-Pekka; Özler, Berk; Seage, George R; Smith, Thomas A; Vespignani, Alessandro; Vynnycky, Emilia; Lipsitch, Marc

2017-12-29

Interventions in infectious diseases can have both direct effects on individuals who receive the intervention as well as indirect effects in the population. In addition, intervention combinations can have complex interactions at the population level, which are often difficult to adequately assess with standard study designs and analytical methods. Herein, we urge the adoption of a new paradigm for the design and interpretation of intervention trials in infectious diseases, particularly with regard to emerging infectious diseases, one that more accurately reflects the dynamics of the transmission process. In an increasingly complex world, simulations can explicitly represent transmission dynamics, which are critical for proper trial design and interpretation. Certain ethical aspects of a trial can also be quantified using simulations. Further, after a trial has been conducted, simulations can be used to explore the possible explanations for the observed effects. Much is to be gained through a multidisciplinary approach that builds collaborations among experts in infectious disease dynamics, epidemiology, statistical science, economics, simulation methods, and the conduct of clinical trials.

The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

PubMed

Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

2008-01-28

To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

How far in-silico computing meets real experiments. A study on the structure and dynamics of spin labeled vinculin tail protein by molecular dynamics simulations and EPR spectroscopy

PubMed Central

2013-01-01

Background Investigation of conformational changes in a protein is a prerequisite to understand its biological function. To explore these conformational changes in proteins we developed a strategy with the combination of molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy. The major goal of this work is to investigate how far computer simulations can meet the experiments. Methods Vinculin tail protein is chosen as a model system as conformational changes within the vinculin protein are believed to be important for its biological function at the sites of cell adhesion. MD simulations were performed on vinculin tail protein both in water and in vacuo environments. EPR experimental data is compared with those of the simulated data for corresponding spin label positions. Results The calculated EPR spectra from MD simulations trajectories of selected spin labelled positions are comparable to experimental EPR spectra. The results show that the information contained in the spin label mobility provides a powerful means of mapping protein folds and their conformational changes. Conclusions The results suggest the localization of dynamic and flexible regions of the vinculin tail protein. This study shows MD simulations can be used as a complementary tool to interpret experimental EPR data. PMID:23445506

Light-induced nonadiabatic dynamics in molecular assemblies and nanostructures

NASA Astrophysics Data System (ADS)

Mitric, Roland

The combination of mixed quantum-classical dynamics with efficient electronic structure methods was developed in order to simulate the light-induced processes in complex molecules, multichromophoric aggregates and metallic nanostructures. We will demonstrate how the combination of nonadiabatic dynamics with experimental pump-probe techniques such as time-resolved photoelectron imaging (TRPEI) allows to fully resolve the mechanism of excited state relaxation through conical intersections in several prototype organic- and biomolecules. Specifically, the role of the solvent in the excited state relaxation in microsolvated and fully solvated systems will be addressed. Currently there is growing evidence that nonadiabatic relaxation processes also play a fundamental role in determining the efficiency of excitonic transfer or charge injection in multichromophoric assemblies. Since such systems are currently out of the reach of the state-of-the-art quantum chemistry a development of even more efficient quantum chemical approaches is necessary in order to describe the excited state dynamics in such assemblies. For this purpose we have recently developed long-range corrected time-dependent density functional tight binding (LC-TDDFTB) nonadiabatic dynamics and combined it with the QM/MM approach in order to simulate exciton relaxation in complex systems. The applications of the method to the investigation of the optical properties and dynamics in multichromophoric assemblies including stacked pi-conjugated organic chromophores, model molecular crystals as well as self-organized dye aggregates will be presented. Finally, we will address exciton transport dynamics coupled with the light propagation in hybrid exciton-plasmon nanostructures, which represent promising materials fort the development of novel light-harvesting systems.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE PAGES

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

2015-06-26

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Dynamic simulations of geologic materials using combined FEM/DEM/SPH analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morris, J P; Johnson, S M

2008-03-26

An overview of the Lawrence Discrete Element Code (LDEC) is presented, and results from a study investigating the effect of explosive and impact loading on geologic materials using the Livermore Distinct Element Code (LDEC) are detailed. LDEC was initially developed to simulate tunnels and other structures in jointed rock masses using large numbers of polyhedral blocks. Many geophysical applications, such as projectile penetration into rock, concrete targets, and boulder fields, require a combination of continuum and discrete methods in order to predict the formation and interaction of the fragments produced. In an effort to model this class of problems, LDECmore » now includes implementations of Cosserat point theory and cohesive elements. This approach directly simulates the transition from continuum to discontinuum behavior, thereby allowing for dynamic fracture within a combined finite element/discrete element framework. In addition, there are many application involving geologic materials where fluid-structure interaction is important. To facilitate solution of this class of problems a Smooth Particle Hydrodynamics (SPH) capability has been incorporated into LDEC to simulate fully coupled systems involving geologic materials and a saturating fluid. We will present results from a study of a broad range of geomechanical problems that exercise the various components of LDEC in isolation and in tandem.« less

Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy.

PubMed

Xu, Yao; Havenith, Martina

2015-11-07

Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Yao; Havenith, Martina

2015-11-01

Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived frommore » fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.« less

MCTDH on-the-fly: Efficient grid-based quantum dynamics without pre-computed potential energy surfaces

NASA Astrophysics Data System (ADS)

Richings, Gareth W.; Habershon, Scott

2018-04-01

We present significant algorithmic improvements to a recently proposed direct quantum dynamics method, based upon combining well established grid-based quantum dynamics approaches and expansions of the potential energy operator in terms of a weighted sum of Gaussian functions. Specifically, using a sum of low-dimensional Gaussian functions to represent the potential energy surface (PES), combined with a secondary fitting of the PES using singular value decomposition, we show how standard grid-based quantum dynamics methods can be dramatically accelerated without loss of accuracy. This is demonstrated by on-the-fly simulations (using both standard grid-based methods and multi-configuration time-dependent Hartree) of both proton transfer on the electronic ground state of salicylaldimine and the non-adiabatic dynamics of pyrazine.

Optimising the Parallelisation of OpenFOAM Simulations

DTIC Science & Technology

2014-06-01

UNCLASSIFIED UNCLASSIFIED Optimising the Parallelisation of OpenFOAM Simulations Shannon Keough Maritime Division Defence...Science and Technology Organisation DSTO-TR-2987 ABSTRACT The OpenFOAM computational fluid dynamics toolbox allows parallel computation of...performance of a given high performance computing cluster with several OpenFOAM cases, running using a combination of MPI libraries and corresponding MPI

Thermodynamic Insights into Effects of Water Displacement and Rearrangement upon Ligand Modification using Molecular Dynamics Simulations.

PubMed

Wahl, Joel; Smiesko, Martin

2018-05-04

Computational methods, namely Molecular Dynamics Simulations (MD simulations) in combination with Inhomogeneous Fluid Solvation Theory (IFST) were used to retrospectively investigate various cases of ligand structure modifications that led to the displacement of binding site water molecules. Our findings are that the water displacement per se is energetically unfavorable in the discussed examples, and that it is merely the fine balance between change in protein-ligand interaction energy, ligand solvation free energies and binding site solvation free energies that determine if water displacement is favorable or not. We furthermore evaluated if we can reproduce experimental binding affinities by a computational approach combining changes in solvation free energies with changes in protein-ligand interaction energies and entropies. In two of the seven cases, this estimation led to large errors, implying that accurate predictions of relative binding free energies based on solvent thermodynamics is challenging. Still, MD simulations can provide insights into which water molecules can be targeted for displacement. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions

NASA Astrophysics Data System (ADS)

Ngaojampa, C.; Nimmanpipug, P.; Yu, L. D.; Anuntalabhochai, S.; Lee, V. S.

2011-02-01

In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the molecular implications of mutation bias. The simulations were focused on the responses of the DNA backbones and nitrogenous bases to irradiation. Analyses of the root mean square displacements of the backbones and non-hydrogen atoms of base rings of the simulated DNA structure after irradiation revealed a potential preference of DNA double strand separation, dependent on the irradiating energy. The results show that for the backbones, the large difference in the displacement between poly-GC and poly-AT in the initial time period could be the reason for the backbone breakage; for the nitrogenous base pairs, A-T is 30% more sensitive or vulnerable to ion irradiation than G-C, demonstrating a preferential, instead of random, effect of irradiation-induced mutation.

Modelling, simulation and applications of longitudinal train dynamics

NASA Astrophysics Data System (ADS)

Cole, Colin; Spiryagin, Maksym; Wu, Qing; Sun, Yan Quan

2017-10-01

Significant developments in longitudinal train simulation and an overview of the approaches to train models and modelling vehicle force inputs are firstly presented. The most important modelling task, that of the wagon connection, consisting of energy absorption devices such as draft gears and buffers, draw gear stiffness, coupler slack and structural stiffness is then presented. Detailed attention is given to the modelling approaches for friction wedge damped and polymer draft gears. A significant issue in longitudinal train dynamics is the modelling and calculation of the input forces - the co-dimensional problem. The need to push traction performances higher has led to research and improvement in the accuracy of traction modelling which is discussed. A co-simulation method that combines longitudinal train simulation, locomotive traction control and locomotive vehicle dynamics is presented. The modelling of other forces, braking propulsion resistance, curve drag and grade forces are also discussed. As extensions to conventional longitudinal train dynamics, lateral forces and coupler impacts are examined in regards to interaction with wagon lateral and vertical dynamics. Various applications of longitudinal train dynamics are then presented. As an alternative to the tradition single wagon mass approach to longitudinal train dynamics, an example incorporating fully detailed wagon dynamics is presented for a crash analysis problem. Further applications of starting traction, air braking, distributed power, energy analysis and tippler operation are also presented.

Simulation of X-ray transient absorption for following vibrations in coherently ionized F2 molecules

NASA Astrophysics Data System (ADS)

Dutoi, Anthony D.; Leone, Stephen R.

2017-01-01

Femtosecond and attosecond X-ray transient absorption experiments are becoming increasingly sophisticated tools for probing nuclear dynamics. In this work, we explore and develop theoretical tools needed for interpretation of such spectra,in order to characterize the vibrational coherences that result from ionizing a molecule in a strong IR field. Ab initio data for F2 is combined with simulations of nuclear dynamics, in order to simulate time-resolved X-ray absorption spectra for vibrational wavepackets after coherent ionization at 0 K and at finite temperature. Dihalogens pose rather difficult electronic structure problems, and the issues encountered in this work will be reflective of those encountered with any core-valence excitation simulation when a bond is breaking. The simulations reveal a strong dependence of the X-ray absorption maximum on the locations of the vibrational wave packets. A Fourier transform of the simulated signal shows features at the overtone frequencies of both the neutral and the cation, which reflect spatial interferences of the vibrational eigenstates. This provides a direct path for implementing ultrafast X-ray spectroscopic methods to visualize coherent nuclear dynamics.

Li + transport in poly(ethylene oxide) based electrolyte: A combined study of neutron scattering, dielectric spectroscopy, and MD simulation

NASA Astrophysics Data System (ADS)

Do, Changwoo; Lunkenheimer, Peter; Diddens, Diddo; Götz, Marion; Weiß, Matthias; Loidl, Alois; Sun, Xiao-Guang; Allgaier, Jürgen; Ohl, Michael

2013-03-01

Dynamics of Li + transport in polyethylene oxide (PEO) and lithium bis(trifluoromethanesulfonyl)imde (LiTFSI) mixtures are investigated by combining various experimental techniques (neutron spin-echo and dielectric spectroscopy) with molecular dynamics (MD) simulations. Our results suggest that the characteristic live times within the cages formed by oxygens are mainly determined by the alpha-relaxation which corresponds to local segmental motions of polymers, to a much lesser extent by the main chain relaxation, and not at all by the beta-relaxation or any other faster processes. The significant contribution of Li + hopping process to the ion conductivity is also identified. Subsequently, detailed characteristic length and time scales of various Li + transport processes in solid polymer electrolytes are presented and interpreted.

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

2017-07-01

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project

Automatic Screening for Perturbations in Boolean Networks.

PubMed

Schwab, Julian D; Kestler, Hans A

2018-01-01

A common approach to address biological questions in systems biology is to simulate regulatory mechanisms using dynamic models. Among others, Boolean networks can be used to model the dynamics of regulatory processes in biology. Boolean network models allow simulating the qualitative behavior of the modeled processes. A central objective in the simulation of Boolean networks is the computation of their long-term behavior-so-called attractors. These attractors are of special interest as they can often be linked to biologically relevant behaviors. Changing internal and external conditions can influence the long-term behavior of the Boolean network model. Perturbation of a Boolean network by stripping a component of the system or simulating a surplus of another element can lead to different attractors. Apparently, the number of possible perturbations and combinations of perturbations increases exponentially with the size of the network. Manually screening a set of possible components for combinations that have a desired effect on the long-term behavior can be very time consuming if not impossible. We developed a method to automatically screen for perturbations that lead to a user-specified change in the network's functioning. This method is implemented in the visual simulation framework ViSiBool utilizing satisfiability (SAT) solvers for fast exhaustive attractor search.

Airborne Detection and Dynamic Modeling of Carbon Dioxide and Methane Plumes

NASA Astrophysics Data System (ADS)

Jacob, Jamey; Mitchell, Taylor; Whyte, Seabrook

2015-11-01

To facilitate safe storage of greenhouse gases such as CO2 and CH4, airborne monitoring is investigated. Conventional soil gas monitoring has difficulty in distinguishing gas flux signals from leakage with those associated with meteorologically driven changes. A low-cost, lightweight sensor system has been developed and implemented onboard a small unmanned aircraft that measures gas concentration and is combined with other atmospheric diagnostics, including thermodynamic data and velocity from hot-wire and multi-hole probes. To characterize the system behavior and verify its effectiveness, field tests have been conducted over controlled rangeland burns and over simulated leaks. In the former case, since fire produces carbon dioxide over a large area, this was an opportunity to test in an environment that while only vaguely similar to a carbon sequestration leak source, also exhibits interesting plume behavior. In the simulated field tests, compressed gas tanks are used to mimic leaks and generate gaseous plumes. Since the sensor response time is a function of vehicle airspeed, dynamic calibration models are required to determine accurate location of gas concentration in (x , y , z , t) . Results are compared with simulations using combined flight and atmospheric dynamic models. Supported by Department of Energy Award DE-FE0012173.

Design and performance evaluation of a simplified dynamic model for combined sewer overflows in pumped sewer systems

NASA Astrophysics Data System (ADS)

van Daal-Rombouts, Petra; Sun, Siao; Langeveld, Jeroen; Bertrand-Krajewski, Jean-Luc; Clemens, François

2016-07-01

Optimisation or real time control (RTC) studies in wastewater systems increasingly require rapid simulations of sewer systems in extensive catchments. To reduce the simulation time calibrated simplified models are applied, with the performance generally based on the goodness of fit of the calibration. In this research the performance of three simplified and a full hydrodynamic (FH) model for two catchments are compared based on the correct determination of CSO event occurrences and of the total discharged volumes to the surface water. Simplified model M1 consists of a rainfall runoff outflow (RRO) model only. M2 combines the RRO model with a static reservoir model for the sewer behaviour. M3 comprises the RRO model and a dynamic reservoir model. The dynamic reservoir characteristics were derived from FH model simulations. It was found that M2 and M3 are able to describe the sewer behaviour of the catchments, contrary to M1. The preferred model structure depends on the quality of the information (geometrical database and monitoring data) available for the design and calibration of the model. Finally, calibrated simplified models are shown to be preferable to uncalibrated FH models when performing optimisation or RTC studies.

A comparison of East Asian summer monsoon simulations from CAM3.1 with three dynamic cores

NASA Astrophysics Data System (ADS)

Wei, Ting; Wang, Lanning; Dong, Wenjie; Dong, Min; Zhang, Jingyong

2011-12-01

This paper examines the sensitivity of CAM3.1 simulations of East Asian summer monsoon (EASM) to the choice of dynamic cores using three long-term simulations, one with each of the following cores: the Eulerian spectral transform method (EUL), semi-Lagrangian scheme (SLD) and finite volume approach (FV). Our results indicate that the dynamic cores significantly influence the simulated fields not only through dynamics, such as wind, but also through physical processes, such as precipitation. Generally speaking, SLD is superior to EUL and FV in simulating the climatological features of EASM and its interannual variability. The SLD version of the CAM model partially reduces its known deficiency in simulating the climatological features of East Asian summer precipitation. The strength and position of simulated western Pacific subtropical high (WPSH) and its ridge line compare more favourably with observations in SLD and FV than in EUL. They contribute to the intensification of the south-easterly along the south of WPSH and the vertical motion through the troposphere around 30° N, where the subtropical rain belt exists. Additionally, SLD simulates the scope of the westerly jet core over East Asia more realistically than the other two dynamic cores do. Considerable systematic errors of the seasonal migration of monsoon rain belt and water vapour flux exist in all of the three versions of CAM3.1 model, although it captures the broad northward shift of convection, and the simulated results share similarities. The interannual variation of EASM is found to be more accurate in SLD simulation, which reasonably reproduces the leading combined patterns of precipitation and 850-hPa winds in East Asia, as well as the 2.5- and 10-year periods of Li-Zeng EASM index. These results emphasise the importance of dynamic cores for the EASM simulation as distinct from the simulation's sensitivity to the physical parameterisations.

The contribution of visual and proprioceptive information to the perception of leaning in a dynamic motorcycle simulator.

PubMed

Lobjois, Régis; Dagonneau, Virginie; Isableu, Brice

2016-11-01

Compared with driving or flight simulation, little is known about self-motion perception in riding simulation. The goal of this study was to examine whether or not continuous roll motion supports the sensation of leaning into bends in dynamic motorcycle simulation. To this end, riders were able to freely tune the visual scene and/or motorcycle simulator roll angle to find a pattern that matched their prior knowledge. Our results revealed idiosyncrasy in the combination of visual and proprioceptive information. Some subjects relied more on the visual dimension, but reported increased sickness symptoms with the visual roll angle. Others relied more on proprioceptive information, tuning the direction of the visual scenery to match three possible patterns. Our findings also showed that these two subgroups tuned the motorcycle simulator roll angle in a similar way. This suggests that sustained inertially specified roll motion have contributed to the sensation of leaning in spite of the occurrence of unexpected gravito-inertial stimulation during the tilt. Several hypotheses are discussed. Practitioner Summary: Self-motion perception in motorcycle simulation is a relatively new research area. We examined how participants combined visual and proprioceptive information. Findings revealed individual differences in the visual dimension. However, participants tuned the simulator roll angle similarly, supporting the hypothesis that sustained inertially specified roll motion contributes to a leaning sensation.

Predicting Drug Combination Index and Simulating the Network-Regulation Dynamics by Mathematical Modeling of Drug-Targeted EGFR-ERK Signaling Pathway

NASA Astrophysics Data System (ADS)

Huang, Lu; Jiang, Yuyang; Chen, Yuzong

2017-01-01

Synergistic drug combinations enable enhanced therapeutics. Their discovery typically involves the measurement and assessment of drug combination index (CI), which can be facilitated by the development and applications of in-silico CI predictive tools. In this work, we developed and tested the ability of a mathematical model of drug-targeted EGFR-ERK pathway in predicting CIs and in analyzing multiple synergistic drug combinations against observations. Our mathematical model was validated against the literature reported signaling, drug response dynamics, and EGFR-MEK drug combination effect. The predicted CIs and combination therapeutic effects of the EGFR-BRaf, BRaf-MEK, FTI-MEK, and FTI-BRaf inhibitor combinations showed consistent synergism. Our results suggest that existing pathway models may be potentially extended for developing drug-targeted pathway models to predict drug combination CI values, isobolograms, and drug-response surfaces as well as to analyze the dynamics of individual and combinations of drugs. With our model, the efficacy of potential drug combinations can be predicted. Our method complements the developed in-silico methods (e.g. the chemogenomic profile and the statistically-inferenced network models) by predicting drug combination effects from the perspectives of pathway dynamics using experimental or validated molecular kinetic constants, thereby facilitating the collective prediction of drug combination effects in diverse ranges of disease systems.

Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

DOE PAGES

Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; ...

2017-01-26

When using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. Furthermore, by calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. A comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnonsmore » leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.« less

Fully compressible solutions for early stage Richtmyer–Meshkov instability

DOE PAGES

Margolin, Len G.; Reisner, Jon Michael

2016-10-27

Here, we will consider the effects of compressibility and viscosity on the early dynamics of the Richtmyer–Meshkov instability (RMI). In particular, we will combine theory, scaling, and high resolution simulation of RMI to probe the details of the initial compression and the subsequent viscous damping as a shock interacts with a density discontinuity. We will propose a refinement of the classic 1D model for the linear regime of RMI that, for small initial perturbation wavelengths, more accurately reproduces the 2D dynamics of a fully resolved numerical simulation.

Space construction base control system

NASA Technical Reports Server (NTRS)

Kaczynski, R. F.

1979-01-01

Several approaches for an attitude control system are studied and developed for a large space construction base that is structurally flexible. Digital simulations were obtained using the following techniques: (1) the multivariable Nyquist array method combined with closed loop pole allocation, (2) the linear quadratic regulator method. Equations for the three-axis simulation using the multilevel control method were generated and are presented. Several alternate control approaches are also described. A technique is demonstrated for obtaining the dynamic structural properties of a vehicle which is constructed of two or more submodules of known dynamic characteristics.

Initial Beam Dynamics Simulations of a High-Average-Current Field-Emission Electron Source in a Superconducting RadioFrequency Gun

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohsen, O.; Gonin, I.; Kephart, R.

High-power electron beams are sought-after tools in support to a wide array of societal applications. This paper investigates the production of high-power electron beams by combining a high-current field-emission electron source to a superconducting radio-frequency (SRF) cavity. We especially carry out beam-dynamics simulations that demonstrate the viability of the scheme to formmore » $$\\sim$$ 300 kW average-power electron beam using a 1+1/2-cell SRF gun.« less

Using Dynamic Simulation to Evaluate Attemperator Operation in a Natural Gas Combined Cycle With Duct Burners in the Heat Recovery Steam Generator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liese, Eric; Zitney, Stephen E.

A generic training simulator of a natural gas combined cycle was modified to match operations at a real plant. The objective was to use the simulator to analyze cycling operations of the plant. Initial operation of the simulator revealed the potential for saturation conditions in the final high pressure superheater as the attemperator tried to control temperature at the superheater outlet during gas turbine loading and unloading. Subsequent plant operational data confirmed simulation results. Multiple simulations were performed during loading and unloading of the gas turbine to determine operational strategies that prevented saturation and increased the approach to saturation temperature.more » The solutions included changes to the attemperator temperature control setpoints and strategic control of the steam turbine inlet pressure control valve.« less

Evaluation of stormwater micropollutant source control and end-of-pipe control strategies using an uncertainty-calibrated integrated dynamic simulation model.

PubMed

Vezzaro, L; Sharma, A K; Ledin, A; Mikkelsen, P S

2015-03-15

The estimation of micropollutant (MP) fluxes in stormwater systems is a fundamental prerequisite when preparing strategies to reduce stormwater MP discharges to natural waters. Dynamic integrated models can be important tools in this step, as they can be used to integrate the limited data provided by monitoring campaigns and to evaluate the performance of different strategies based on model simulation results. This study presents an example where six different control strategies, including both source-control and end-of-pipe treatment, were compared. The comparison focused on fluxes of heavy metals (copper, zinc) and organic compounds (fluoranthene). MP fluxes were estimated by using an integrated dynamic model, in combination with stormwater quality measurements. MP sources were identified by using GIS land usage data, runoff quality was simulated by using a conceptual accumulation/washoff model, and a stormwater retention pond was simulated by using a dynamic treatment model based on MP inherent properties. Uncertainty in the results was estimated with a pseudo-Bayesian method. Despite the great uncertainty in the MP fluxes estimated by the runoff quality model, it was possible to compare the six scenarios in terms of discharged MP fluxes, compliance with water quality criteria, and sediment accumulation. Source-control strategies obtained better results in terms of reduction of MP emissions, but all the simulated strategies failed in fulfilling the criteria based on emission limit values. The results presented in this study shows how the efficiency of MP pollution control strategies can be quantified by combining advanced modeling tools (integrated stormwater quality model, uncertainty calibration). Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of Solid Fraction on Droplet Wetting and Vapor Condensation: A Molecular Dynamic Simulation Study.

PubMed

Gao, Shan; Liao, Quanwen; Liu, Wei; Liu, Zhichun

2017-10-31

Recently, numerous studies focused on the wetting process of droplets on various surfaces at a microscale level. However, there are a limited number of studies about the mechanism of condensation on patterned surfaces. The present study performed the dynamic wetting behavior of water droplets and condensation process of water molecules on substrates with different pillar structure parameters, through molecular dynamic simulation. The dynamic wetting results indicated that droplets exhibit Cassie state, PW state, and Wenzel state successively on textured surfaces with decreasing solid fraction. The droplets possess a higher static contact angle and a smaller spreading exponent on textured surfaces than those on smooth surfaces. The condensation processes, including the formation, growth, and coalescence of a nanodroplet, are simulated and quantitatively recorded, which are difficult to be observed by experiments. In addition, a wetting transition and a dewetting transition were observed and analyzed in condensation on textured surfaces. Combining these simulation results with previous theoretical and experimental studies will guide us to understand the hypostasis and mechanism of the condensation more clearly.

Ab initio molecular dynamics simulation of LiBr association in water

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Philpott, Michael R.

2000-12-01

A computationally economical scheme which unifies the density functional description of an ionic solute and the classical description of a solvent was developed. The density functional part of the scheme comprises Car-Parrinello and related formalisms. The substantial saving in the computer time is achieved by performing the ab initio molecular dynamics of the solute electronic structure in a relatively small basis set constructed from lowest energy Kohn-Sham orbitals calculated for a single anion in vacuum, instead of using plane wave basis. The methodology permits simulation of an ionic solution for longer time scales while keeping accuracy in the prediction of the solute electronic structure. As an example the association of the Li+-Br- ion-pair system in water is studied. The results of the combined molecular dynamics simulation are compared with that obtained from the classical simulation with ion-ion interaction described by the pair potential of Born-Huggins-Mayer type. The comparison reveals an important role played by the polarization of the Br- ion in the dynamics of ion pair association.

Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal.

PubMed

Shibuta, Yasushi; Sakane, Shinji; Miyoshi, Eisuke; Okita, Shin; Takaki, Tomohiro; Ohno, Munekazu

2017-04-05

Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics-processing-unit rich supercomputer can shed light on this long-standing issue. Here, a billion-atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite-like small grains surrounding previously formed large grains exist in the middle of the nucleation process, which are not distributed uniformly. At the same time, grains with a twin boundary are formed by heterogeneous nucleation from the surface of the previously formed grains. The local heterogeneity in the distribution of grains is caused by the local accumulation of the icosahedral structure in the undercooled melt near the previously formed grains. This insight is mainly attributable to the multi-graphics processing unit parallel computation combined with the rapid progress in high-performance computational environments.Nucleation is a fundamental physical process, however it is a long-standing issue whether completely homogeneous nucleation can occur. Here the authors reveal, via a billion-atom molecular dynamics simulation, that local heterogeneity exists during homogeneous nucleation in an undercooled iron melt.

Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation.

PubMed

Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

2017-02-21

Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation

PubMed Central

Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

2017-01-01

Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance. PMID:28772570

Combined Molecular and Spin Dynamics Simulation of Lattice Vacancies in BCC Iron

NASA Astrophysics Data System (ADS)

Mudrick, Mark; Perera, Dilina; Eisenbach, Markus; Landau, David P.

Using an atomistic model that treats translational and spin degrees of freedom equally, combined molecular and spin dynamics simulations have been performed to study dynamic properties of BCC iron at varying levels of defect impurity. Atomic interactions are described by an empirical many-body potential, and spin interactions with a Heisenberg-like Hamiltonian with a coordinate dependent exchange interaction. Equations of motion are solved numerically using the second-order Suzuki-Trotter decomposition for the time evolution operator. We analyze the spatial and temporal correlation functions for atomic displacements and magnetic order to obtain the effect of vacancy defects on the phonon and magnon excitations. We show that vacancy clusters in the material cause splitting of the characteristic transverse spin-wave excitations, indicating the production of additional excitation modes. Additionally, we investigate the coupling of the atomic and magnetic modes. These modes become more distinct with increasing vacancy cluster size. This material is based upon work supported by the U.S. Department of Energy Office of Science Graduate Student Research (SCGSR) program.

Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study

NASA Astrophysics Data System (ADS)

Cazade, Pierre-André; Tran, Halina; Bereau, Tristan; Das, Akshaya K.; Kläsi, Felix; Hamm, Peter; Meuwly, Markus

2015-06-01

The solvent dynamics around fluorinated acetonitrile is characterized by 2-dimensional infrared spectroscopy and atomistic simulations. The lineshape of the linear infrared spectrum is better captured by semiempirical (density functional tight binding) mixed quantum mechanical/molecular mechanics simulations, whereas force field simulations with multipolar interactions yield lineshapes that are significantly too narrow. For the solvent dynamics, a relatively slow time scale of 2 ps is found from the experiments and supported by the mixed quantum mechanical/molecular mechanics simulations. With multipolar force fields fitted to the available thermodynamical data, the time scale is considerably faster—on the 0.5 ps time scale. The simulations provide evidence for a well established CF-HOH hydrogen bond (population of 25%) which is found from the radial distribution function g(r) from both, force field and quantum mechanics/molecular mechanics simulations.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

PubMed

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

New insights into photodissociation dynamics of cyclobutanone from the AIMS dynamic simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Lihong; Fang, Wei-Hai, E-mail: fangwh@bnu.edu.cn

2016-04-14

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 (S{sub 0}) and the first excited singlet (S{sub 1}) states were determined in the present study, which were confirmed to be the new S{sub 1} → S{sub 0} funnels by the ab initio multiple spawning dynamic simulation, giving rise to products in the S{sub 0} state selectively. The time evolution of the S{sub 1} electronic population was fitted with the pure exponentialmore » formulae, from which the S{sub 1} lifetime was estimated to be 484.0 fs. The time constant for the S{sub 1} α-cleavage is calculated to be 176.6 fs, which is based on the present dynamics simulation. As a result of the ultrafast S{sub 1} processes, the statistical distribution of the excess energies is prevented in the S{sub 1} state. The S{sub 1} 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.« less

Stokes-Einstein relation of the liquid metal rubidium and its relationship to changes in the microscopic dynamics with increasing temperature

NASA Astrophysics Data System (ADS)

Demmel, F.; Tani, A.

2018-06-01

For liquid rubidium the Stokes-Einstein (SE) relation is well fulfilled near the melting point with an effective hydrodynamic diameter, which agrees well with a value from structural investigations. A wealth of thermodynamic and microscopic data exists for a wide range of temperatures for liquid rubidium and hence it represents a good test bed to challenge the SE relation with rising temperature from an experimental point of view. We performed classical molecular dynamics simulations to complement the existing experimental data using a pseudopotential, which describes perfectly the structure and dynamics of liquid rubidium. The derived SE relation from combining experimental shear viscosity data with simulated diffusion coefficients reveals a weak violation at about 1.3 Tmelting≈400 K. The microscopic relaxation dynamics on nearest neighbor distances from neutron spectroscopy demonstrate distinct changes in the amplitude with rising temperature. The derived average relaxation time for density fluctuations on this length scale shows a non-Arrhenius behavior, with a slope change around 1.5 Tmelting≈450 K. Combining the simulated macroscopic self-diffusion coefficient with that microscopic average relaxation time, a distinct violation of the SE relation in the same temperature range can be demonstrated. One can conclude that the changes in the collective dynamics, a mirror of the correlated movements of the particles, are at the origin for the violation of the SE relation. The changes in the dynamics can be understood as a transition from a more viscous liquid metal to a more fluid-like liquid above the crossover temperature range of 1.3-1.5 Tmelting. The decay of the amplitude of density fluctuations in liquid aluminium, lead, and rubidium demonstrates a remarkable agreement and points to a universal thermal crossover in the dynamics of liquid metals.

Analysis of utilization of desert habitats with dynamic simulation

USGS Publications Warehouse

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.

How to assess the impact of a physical parameterization in simulations of moist convection?

NASA Astrophysics Data System (ADS)

Grabowski, Wojciech

2017-04-01

A numerical model capable in simulating moist convection (e.g., cloud-resolving model or large-eddy simulation model) consists of a fluid flow solver combined with required representations (i.e., parameterizations) of physical processes. The later typically include cloud microphysics, radiative transfer, and unresolved turbulent transport. Traditional approaches to investigate impacts of such parameterizations on convective dynamics involve parallel simulations with different parameterization schemes or with different scheme parameters. Such methodologies are not reliable because of the natural variability of a cloud field that is affected by the feedback between the physics and dynamics. For instance, changing the cloud microphysics typically leads to a different realization of the cloud-scale flow, and separating dynamical and microphysical impacts is difficult. This presentation will present a novel modeling methodology, the piggybacking, that allows studying the impact of a physical parameterization on cloud dynamics with confidence. The focus will be on the impact of cloud microphysics parameterization. Specific examples of the piggybacking approach will include simulations concerning the hypothesized deep convection invigoration in polluted environments, the validity of the saturation adjustment in modeling condensation in moist convection, and separation of physical impacts from statistical uncertainty in simulations applying particle-based Lagrangian microphysics, the super-droplet method.

Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.

PubMed

Emperador, Agustí; Orozco, Modesto

2017-03-14

We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.

Simulated Pitot tube designed to detect blockage by ice, volcanic dust, sand, insects and to clear it: phase 1

NASA Astrophysics Data System (ADS)

Jackson, David A.

2014-05-01

A simulated coaxial Pitot tube has been developed using fibre optic sensors combined with actuators to monitor and maintain its correct operation under different environmental conditions. Experiments are reported showing that the dynamic and static tubes can be cleared of ice. It is also demonstrated that the dynamic tube can be cleared of dust and sand which is not the case for the static tube in the coaxial configuration. An approach is proposed to overcome this problem involving a conventional configuration where the static tube is operated independently orthogonal to the dynamic tube with a second set of sensors and actuators.

Embedding of multidimensional time-dependent observations.

PubMed

Barnard, J P; Aldrich, C; Gerber, M

2001-10-01

A method is proposed to reconstruct dynamic attractors by embedding of multivariate observations of dynamic nonlinear processes. The Takens embedding theory is combined with independent component analysis to transform the embedding into a vector space of linearly independent vectors (phase variables). The method is successfully tested against prediction of the unembedded state vector in two case studies of simulated chaotic processes.

Embedding of multidimensional time-dependent observations

NASA Astrophysics Data System (ADS)

Barnard, Jakobus P.; Aldrich, Chris; Gerber, Marius

2001-10-01

A method is proposed to reconstruct dynamic attractors by embedding of multivariate observations of dynamic nonlinear processes. The Takens embedding theory is combined with independent component analysis to transform the embedding into a vector space of linearly independent vectors (phase variables). The method is successfully tested against prediction of the unembedded state vector in two case studies of simulated chaotic processes.

A biologically-based individual tree model for managing the longleaf pine ecosystem

Treesearch

Rick Smith; Greg Somers

1998-01-01

Duration: 1995-present Objective: Develop a longleaf pine dynamics model and simulation system to define desirable ecosystem management practices in existing and future longleaf pine stands. Methods: Naturally-regenerated longleaf pine trees are being destructively sampled to measure their recent growth and dynamics. Soils and climate data will be combined with the...

Molecular dynamics study of the melting curve of NiTi alloy under pressure

NASA Astrophysics Data System (ADS)

Zeng, Zhao-Yi; Hu, Cui-E.; Cai, Ling-Cang; Chen, Xiang-Rong; Jing, Fu-Qian

2011-02-01

The melting curve of NiTi alloy was predicted by using molecular dynamics simulations combining with the embedded atom model potential. The calculated thermal equation of state consists well with our previous results obtained from quasiharmonic Debye approximation. Fitting the well-known Simon form to our Tm data yields the melting curves for NiTi: 1850(1 + P/21.938)0.328 (for one-phase method) and 1575(1 + P/7.476)0.305 (for two-phase method). The two-phase simulations can effectively eliminate the superheating in one-phase simulations. At 1 bar, the melting temperature of NiTi is 1575 ± 25 K and the corresponding melting slope is 64 K/GPa.

Research on dynamic balancing simulation of rotary shaft based on ADAMS

NASA Astrophysics Data System (ADS)

Zheng, Weiqiang; Rui, Chengjie; Yang, Jie; Liu, Pingyi

2018-02-01

Due to the design and processing technology of rotary shaft, the mass center of it does not coincide with the rotating axis of the rotary shaft and there is an unbalanced mass. The unbalanced mass can have some disadvantages, such as the centrifugal force, the vibration and so on. Those disadvantages could reduce the accuracy and service life of the equipment.In this paper, the dynamic balance of the rotary shaft is analysed by the theory analysis combined with the dynamic simulation software. This method ensures that the rotary shaft meets the dynamic balancing requirements during the design stage. It effectively supports the structural design of the rotary shift, and provides a way of thinking and method for the design and development of the same type of products.

Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations.

PubMed

Stock, Philipp; Monroe, Jacob I; Utzig, Thomas; Smith, David J; Shell, M Scott; Valtiner, Markus

2017-03-28

Interactions between hydrophobic moieties steer ubiquitous processes in aqueous media, including the self-organization of biologic matter. Recent decades have seen tremendous progress in understanding these for macroscopic hydrophobic interfaces. Yet, it is still a challenge to experimentally measure hydrophobic interactions (HIs) at the single-molecule scale and thus to compare with theory. Here, we present a combined experimental-simulation approach to directly measure and quantify the sequence dependence and additivity of HIs in peptide systems at the single-molecule scale. We combine dynamic single-molecule force spectroscopy on model peptides with fully atomistic, both equilibrium and nonequilibrium, molecular dynamics (MD) simulations of the same systems. Specifically, we mutate a flexible (GS) 5 peptide scaffold with increasing numbers of hydrophobic leucine monomers and measure the peptides' desorption from hydrophobic self-assembled monolayer surfaces. Based on the analysis of nonequilibrium work-trajectories, we measure an interaction free energy that scales linearly with 3.0-3.4 k B T per leucine. In good agreement, simulations indicate a similar trend with 2.1 k B T per leucine, while also providing a detailed molecular view into HIs. This approach potentially provides a roadmap for directly extracting qualitative and quantitative single-molecule interactions at solid/liquid interfaces in a wide range of fields, including interactions at biointerfaces and adhesive interactions in industrial applications.

Simulation of Mercury's magnetosheath with a combined hybrid-paraboloid model

NASA Astrophysics Data System (ADS)

Parunakian, David; Dyadechkin, Sergey; Alexeev, Igor; Belenkaya, Elena; Khodachenko, Maxim; Kallio, Esa; Alho, Markku

2017-08-01

In this paper we introduce a novel approach for modeling planetary magnetospheres that involves a combination of the hybrid model and the paraboloid magnetosphere model (PMM); we further refer to it as the combined hybrid model. While both of these individual models have been successfully applied in the past, their combination enables us both to overcome the traditional difficulties of hybrid models to develop a self-consistent magnetic field and to compensate the lack of plasma simulation in the PMM. We then use this combined model to simulate Mercury's magnetosphere and investigate the geometry and configuration of Mercury's magnetosheath controlled by various conditions in the interplanetary medium. The developed approach provides a unique comprehensive view of Mercury's magnetospheric environment for the first time. Using this setup, we compare the locations of the bow shock and the magnetopause as determined by simulations with the locations predicted by stand-alone PMM runs and also verify the magnetic and dynamic pressure balance at the magnetopause. We also compare the results produced by these simulations with observational data obtained by the magnetometer on board the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft along a dusk-dawn orbit and discuss the signatures of the magnetospheric features that appear in these simulations. Overall, our analysis suggests that combining the semiempirical PMM with a self-consistent global kinetic model creates new modeling possibilities which individual models cannot provide on their own.

Conduit dynamics and post explosion degassing on Stromboli: A combined UV camera and numerical modeling treatment

PubMed Central

McGonigle, A. J. S.; James, M. R.; Tamburello, G.; Aiuppa, A.; Delle Donne, D.; Ripepe, M.

2016-01-01

Abstract Recent gas flux measurements have shown that Strombolian explosions are often followed by periods of elevated flux, or “gas codas,” with durations of order a minute. Here we present UV camera data from 200 events recorded at Stromboli volcano to constrain the nature of these codas for the first time, providing estimates for combined explosion plus coda SO2 masses of ≈18–225 kg. Numerical simulations of gas slug ascent show that substantial proportions of the initial gas mass can be distributed into a train of “daughter bubbles” released from the base of the slug, which we suggest, generate the codas, on bursting at the surface. This process could also cause transitioning of slugs into cap bubbles, significantly reducing explosivity. This study is the first attempt to combine high temporal resolution gas flux data with numerical simulations of conduit gas flow to investigate volcanic degassing dynamics. PMID:27478285

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

NASA Astrophysics Data System (ADS)

Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik

2016-08-01

Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.

Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

PubMed

Fujisaki, Hiroshi; Moritsugu, Kei; Matsunaga, Yasuhiro; Morishita, Tetsuya; Maragliano, Luca

2015-01-01

Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.

Detonation initiation in a model of explosive: Comparative atomistic and hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Murzov, S. A.; Sergeev, O. V.; Dyachkov, S. A.; Egorova, M. S.; Parshikov, A. N.; Zhakhovsky, V. V.

2016-11-01

Here we extend consistent simulations to reactive materials by the example of AB model explosive. The kinetic model of chemical reactions observed in a molecular dynamics (MD) simulation of self-sustained detonation wave can be used in hydrodynamic simulation of detonation initiation. Kinetic coefficients are obtained by minimization of difference between profiles of species calculated from the kinetic model and observed in MD simulations of isochoric thermal decomposition with a help of downhill simplex method combined with random walk in multidimensional space of fitting kinetic model parameters.

Design and landing dynamic analysis of reusable landing leg for a near-space manned capsule

NASA Astrophysics Data System (ADS)

Yue, Shuai; Nie, Hong; Zhang, Ming; Wei, Xiaohui; Gan, Shengyong

2018-06-01

To improve the landing performance of a near-space manned capsule under various landing conditions, a novel landing system is designed that employs double chamber and single chamber dampers in the primary and auxiliary struts, respectively. A dynamic model of the landing system is established, and the damper parameters are determined by employing the design method. A single-leg drop test with different initial pitch angles is then conducted to compare and validate the simulation model. Based on the validated simulation model, seven critical landing conditions regarding nine crucial landing responses are found by combining the radial basis function (RBF) surrogate model and adaptive simulated annealing (ASA) optimization method. Subsequently, the adaptability of the landing system under critical landing conditions is analyzed. The results show that the simulation effectively results match the test results, which validates the accuracy of the dynamic model. In addition, all of the crucial responses under their corresponding critical landing conditions satisfy the design specifications, demonstrating the feasibility of the landing system.

Magnon and phonon dispersion, lifetime, and thermal conductivity of iron from spin-lattice dynamics simulations

NASA Astrophysics Data System (ADS)

Wu, Xufei; Liu, Zeyu; Luo, Tengfei

2018-02-01

In recent years, the fundamental physics of spin-lattice (e.g., magnon-phonon) interaction has attracted significant experimental and theoretical interests given its potential paradigm-shifting impacts in areas like spin-thermoelectrics, spin-caloritronics, and spintronics. Modelling studies of the transport of magnons and phonons in magnetic crystals are very rare. In this paper, we use spin-lattice dynamics (SLD) simulations to model ferromagnetic crystalline iron, where the spin and lattice systems are coupled through the atomic position-dependent exchange function, and thus the interaction between magnons and phonons is naturally considered. We then present a method combining SLD simulations with spectral energy analysis to calculate the magnon and phonon harmonic (e.g., dispersion, specific heat, and group velocity) and anharmonic (e.g., scattering rate) properties, based on which their thermal conductivity values are calculated. This work represents an example of using SLD simulations to understand the transport properties involving coupled magnon and phonon dynamics.

Efficient Brownian Dynamics of rigid colloids in linear flow fields based on the grand mobility matrix

NASA Astrophysics Data System (ADS)

Palanisamy, Duraivelan; den Otter, Wouter K.

2018-05-01

We present an efficient general method to simulate in the Stokesian limit the coupled translational and rotational dynamics of arbitrarily shaped colloids subject to external potential forces and torques, linear flow fields, and Brownian motion. The colloid's surface is represented by a collection of spherical primary particles. The hydrodynamic interactions between these particles, here approximated at the Rotne-Prager-Yamakawa level, are evaluated only once to generate the body's (11 × 11) grand mobility matrix. The constancy of this matrix in the body frame, combined with the convenient properties of quaternions in rotational Brownian Dynamics, enables an efficient simulation of the body's motion. Simulations in quiescent fluids yield correct translational and rotational diffusion behaviour and sample Boltzmann's equilibrium distribution. Simulations of ellipsoids and spherical caps under shear, in the absence of thermal fluctuations, yield periodic orbits in excellent agreement with the theories by Jeffery and Dorrepaal. The time-varying stress tensors provide the Einstein coefficient and viscosity of dilute suspensions of these bodies.

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Combined distribution functions: A powerful tool to identify cation coordination geometries in liquid systems

NASA Astrophysics Data System (ADS)

Sessa, Francesco; D'Angelo, Paola; Migliorati, Valentina

2018-01-01

In this work we have developed an analytical procedure to identify metal ion coordination geometries in liquid media based on the calculation of Combined Distribution Functions (CDFs) starting from Molecular Dynamics (MD) simulations. CDFs provide a fingerprint which can be easily and unambiguously assigned to a reference polyhedron. The CDF analysis has been tested on five systems and has proven to reliably identify the correct geometries of several ion coordination complexes. This tool is simple and general and can be efficiently applied to different MD simulations of liquid systems.

Experimentally simulating the dynamics of quantum light and matter at ultrastrong coupling using circuit QED (2) - light dynamics and light-matter entanglement -

NASA Astrophysics Data System (ADS)

Sagastizabal, R.; Langford, N. K.; Kounalakis, M.; Dickel, C.; Bruno, A.; Luthi, F.; Thoen, D. J.; Endo, A.; Dicarlo, L.

Light-matter interaction can lead to large photon build-up and hybrid atom-photon entanglement in the ultrastrong coupling (USC) regime, where the coupling strength becomes comparable to the eigenenergies of the system. Accessing the cavity degree of freedom, however, is an outstanding challenge in natural USC systems. In this talk, we directly probe light field dynamics in the USC regime using a digital simulation of the quantum Rabi model in a planar circuit QED chip with a transmon moderately coupled to a resonator. We produce high-accuracy USC light-matter dynamics, using second-order Trotterisation and up to 90 Trotter steps. We probe the average photon number, photon parity and perform Wigner tomography of the simulated field. Finally, we combine tomography of the resonator with qubit measurements to evidence the Schrödinger-cat-like atom-photon entanglement which is a key signature of light-matter dynamics in the USC regime. Funding from the EU FP7 Project ScaleQIT, the ERC Synergy Grant QC-lab, the Netherlands Organization of Scientic Research (NWO), and Microsoft Research.

Calorimetric, FTIR and 1H NMR measurements in combination with DFT calculations for monitoring solid-state changes of dynamics of sibutramine hydrochloride.

PubMed

Pajzderska, Aleksandra; Chudoba, Dorota M; Mielcarek, Jadwiga; Wąsicki, Jan

2012-10-01

Two forms of sibutramine hydrochloride, monohydrate and anhydrous, have been investigated by calorimetric methods, Fourier transform infrared (FTIR) absorption and (1) H nuclear magnetic resonance (NMR) measurements as well as by density functional theory (DFT) of vibrational frequencies and infrared intensities, calculations of steric hindrances and Monte Carlo simulations. The results of FTIR spectra combined with DFT calculations permitted identification of the bands corresponding to the dynamics and vibrations of water molecules. NMR study and Monte Carlo simulations revealed the occurrence of reorientation jumps of the methyl groups in sibutramine cation and also revealed that the reorientation of isopropyl group is possible only in sibutramine monohydrate hydrochloride. The hydration of sibutramine hydrochloride causes a change in the conformation of sibutramine cation. Copyright © 2012 Wiley-Liss, Inc.

Adaptive polarization image fusion based on regional energy dynamic weighted average

NASA Astrophysics Data System (ADS)

Zhao, Yong-Qiang; Pan, Quan; Zhang, Hong-Cai

2005-11-01

According to the principle of polarization imaging and the relation between Stokes parameters and the degree of linear polarization, there are much redundant and complementary information in polarized images. Since man-made objects and natural objects can be easily distinguished in images of degree of linear polarization and images of Stokes parameters contain rich detailed information of the scene, the clutters in the images can be removed efficiently while the detailed information can be maintained by combining these images. An algorithm of adaptive polarization image fusion based on regional energy dynamic weighted average is proposed in this paper to combine these images. Through an experiment and simulations, most clutters are removed by this algorithm. The fusion method is used for different light conditions in simulation, and the influence of lighting conditions on the fusion results is analyzed.

NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics.

PubMed

Shintani, Megumi; Yoshida, Ken; Sakuraba, Shun; Nakahara, Masaru; Matubayasi, Nobuyuki

2011-07-28

Motional correlation times between the hydrophilic and hydrophobic terminal groups in lipid membranes are studied over a wide range of curvatures using the solution-state (1)H NMR-nuclear Overhauser effect (NOE) and molecular dynamics (MD) simulation. To enable (1)H NMR-NOE measurements for large vesicles, the transient NOE method is combined with the spin-echo method, and is successfully applied to a micelle of 1-palmitoyl-lysophosphatidylcholine (PaLPC) with diameter of 5 nm and to vesicles of dipalmitoylphosphatidylcholine (DPPC) with diameters ranging from 30 to 800 nm. It is found that the NOE intensity increases with the diameter up to ∼100 nm, and the model membrane is considered planar on the molecular level beyond ∼100 nm. While the NOE between the hydrophilic terminal and hydrophobic terminal methyl groups is absent for the micelle, its intensity is comparable to that for the neighboring group for vesicles with larger diameters. The origin of NOE signals between distant sites is analyzed by MD simulations of PaLPC micelles and DPPC planar bilayers. The slow relaxation is shown to yield an observable NOE signal even for the hydrophilic and hydrophobic terminal sites. Since the information on distance and dynamics cannot be separated in the experimental NOE alone, the correlation time in large vesicles is determined by combining the experimental NOE intensity and MD-based distance distribution. For large vesicles, the correlation time is found to vary by 2 orders of magnitude over the proton sites. This study shows that NOE provides dynamic information on large vesicles when combined with MD, which provides structural information. © 2011 American Chemical Society

SEARCH: Spatially Explicit Animal Response to Composition of Habitat.

PubMed

Pauli, Benjamin P; McCann, Nicholas P; Zollner, Patrick A; Cummings, Robert; Gilbert, Jonathan H; Gustafson, Eric J

2013-01-01

Complex decisions dramatically affect animal dispersal and space use. Dispersing individuals respond to a combination of fine-scale environmental stimuli and internal attributes. Individual-based modeling offers a valuable approach for the investigation of such interactions because it combines the heterogeneity of animal behaviors with spatial detail. Most individual-based models (IBMs), however, vastly oversimplify animal behavior and such behavioral minimalism diminishes the value of these models. We present program SEARCH (Spatially Explicit Animal Response to Composition of Habitat), a spatially explicit, individual-based, population model of animal dispersal through realistic landscapes. SEARCH uses values in Geographic Information System (GIS) maps to apply rules that animals follow during dispersal, thus allowing virtual animals to respond to fine-scale features of the landscape and maintain a detailed memory of areas sensed during movement. SEARCH also incorporates temporally dynamic landscapes so that the environment to which virtual animals respond can change during the course of a simulation. Animals in SEARCH are behaviorally dynamic and able to respond to stimuli based upon their individual experiences. Therefore, SEARCH is able to model behavioral traits of dispersing animals at fine scales and with many dynamic aspects. Such added complexity allows investigation of unique ecological questions. To illustrate SEARCH's capabilities, we simulated case studies using three mammals. We examined the impact of seasonally variable food resources on the weight distribution of dispersing raccoons (Procyon lotor), the effect of temporally dynamic mortality pressure in combination with various levels of behavioral responsiveness in eastern chipmunks (Tamias striatus), and the impact of behavioral plasticity and home range selection on disperser mortality and weight change in virtual American martens (Martes americana). These simulations highlight the relevance of SEARCH for a variety of applications and illustrate benefits it can provide for conservation planning.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hale, Richard Edward; Cetiner, Sacit M.; Fugate, David L.

The Small Modular Reactor (SMR) Dynamic System Modeling Tool project is in the third year of development. The project is designed to support collaborative modeling and study of various advanced SMR (non-light water cooled) concepts, including the use of multiple coupled reactors at a single site. The objective of the project is to provide a common simulation environment and baseline modeling resources to facilitate rapid development of dynamic advanced reactor SMR models, ensure consistency among research products within the Instrumentation, Controls, and Human-Machine Interface (ICHMI) technical area, and leverage cross-cutting capabilities while minimizing duplication of effort. The combined simulation environmentmore » and suite of models are identified as the Modular Dynamic SIMulation (MoDSIM) tool. The critical elements of this effort include (1) defining a standardized, common simulation environment that can be applied throughout the program, (2) developing a library of baseline component modules that can be assembled into full plant models using existing geometry and thermal-hydraulic data, (3) defining modeling conventions for interconnecting component models, and (4) establishing user interfaces and support tools to facilitate simulation development (i.e., configuration and parameterization), execution, and results display and capture.« less

Simulating Flying Insects Using Dynamics and Data-Driven Noise Modeling to Generate Diverse Collective Behaviors

PubMed Central

Ren, Jiaping; Wang, Xinjie; Manocha, Dinesh

2016-01-01

We present a biologically plausible dynamics model to simulate swarms of flying insects. Our formulation, which is based on biological conclusions and experimental observations, is designed to simulate large insect swarms of varying densities. We use a force-based model that captures different interactions between the insects and the environment and computes collision-free trajectories for each individual insect. Furthermore, we model the noise as a constructive force at the collective level and present a technique to generate noise-induced insect movements in a large swarm that are similar to those observed in real-world trajectories. We use a data-driven formulation that is based on pre-recorded insect trajectories. We also present a novel evaluation metric and a statistical validation approach that takes into account various characteristics of insect motions. In practice, the combination of Curl noise function with our dynamics model is used to generate realistic swarm simulations and emergent behaviors. We highlight its performance for simulating large flying swarms of midges, fruit fly, locusts and moths and demonstrate many collective behaviors, including aggregation, migration, phase transition, and escape responses. PMID:27187068

Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering.

PubMed

Li, Yan; Li, Xiang; Ma, Weiya; Dong, Zigang

2014-08-12

The epidermal growth factor receptor (EGFR) is aberrantly activated in various cancer cells and an important target for cancer treatment. Deep understanding of EGFR conformational changes between the active and inactive states is of pharmaceutical interest. Here we present a strategy combining multiply targeted molecular dynamics simulations, unbiased molecular dynamics simulations, and Bayesian clustering to investigate transition pathways during the activation/inactivation process of EGFR kinase domain. Two distinct pathways between the active and inactive forms are designed, explored, and compared. Based on Bayesian clustering and rough two-dimensional free energy surfaces, the energy-favorable pathway is recognized, though DFG-flip happens in both pathways. In addition, another pathway with different intermediate states appears in our simulations. Comparison of distinct pathways also indicates that disruption of the Lys745-Glu762 interaction is critically important in DFG-flip while movement of the A-loop significantly facilitates the conformational change. Our simulations yield new insights into EGFR conformational transitions. Moreover, our results verify that this approach is valid and efficient in sampling of protein conformational changes and comparison of distinct pathways.

The cultural implications of growth: Modeling nonlinear interaction of trait selection and population dynamics

NASA Astrophysics Data System (ADS)

Antoci, Angelo; Galeotti, Marcello; Russu, Paolo; Luigi Sacco, Pier

2018-05-01

In this paper, we study a nonlinear model of the interaction between trait selection and population dynamics, building on previous work of Ghirlanda et al. [Theor. Popul. Biol. 77, 181-188 (2010)] and Antoci et al. [Commun. Nonlinear Sci. Numer. Simul. 58, 92-106 (2018)]. We establish some basic properties of the model dynamics and present some simulations of the fine-grained structure of alternative dynamic regimes for chosen combinations of parameters. The role of the parameters that govern the reinforcement/corruption of maladaptive vs. adaptive traits is of special importance in determining the model's dynamic evolution. The main implication of this result is the need to pay special attention to the structural forces that may favor the emergence and consolidation of maladaptive traits in contemporary socio-economies, as it is the case, for example, for the stimulation of dysfunctional consumption habits and lifestyles in the pursuit of short-term profits.

Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study.

PubMed

Dhindsa, Gurpreet K; Bhowmik, Debsindhu; Goswami, Monojoy; O'Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang-Qiang

2016-09-14

Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle.

PubMed

Salorinne, Kirsi; Malola, Sami; Wong, O Andrea; Rithner, Christopher D; Chen, Xi; Ackerson, Christopher J; Häkkinen, Hannu

2016-01-21

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of (1)H and (13)C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications.

The cultural implications of growth: Modeling nonlinear interaction of trait selection and population dynamics.

PubMed

Antoci, Angelo; Galeotti, Marcello; Russu, Paolo; Luigi Sacco, Pier

2018-05-01

In this paper, we study a nonlinear model of the interaction between trait selection and population dynamics, building on previous work of Ghirlanda et al. [Theor. Popul. Biol. 77, 181-188 (2010)] and Antoci et al. [Commun. Nonlinear Sci. Numer. Simul. 58, 92-106 (2018)]. We establish some basic properties of the model dynamics and present some simulations of the fine-grained structure of alternative dynamic regimes for chosen combinations of parameters. The role of the parameters that govern the reinforcement/corruption of maladaptive vs. adaptive traits is of special importance in determining the model's dynamic evolution. The main implication of this result is the need to pay special attention to the structural forces that may favor the emergence and consolidation of maladaptive traits in contemporary socio-economies, as it is the case, for example, for the stimulation of dysfunctional consumption habits and lifestyles in the pursuit of short-term profits.

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle

PubMed Central

Salorinne, Kirsi; Malola, Sami; Wong, O. Andrea; Rithner, Christopher D.; Chen, Xi; Ackerson, Christopher J.; Häkkinen, Hannu

2016-01-01

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of 1H and 13C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications. PMID:26791253

Modelling of creep hysteresis in ferroelectrics

NASA Astrophysics Data System (ADS)

He, Xuan; Wang, Dan; Wang, Linxiang; Melnik, Roderick

2018-05-01

In the current paper, a macroscopic model is proposed to simulate the hysteretic dynamics of ferroelectric ceramics with creep phenomenon incorporated. The creep phenomenon in the hysteretic dynamics is attributed to the rate-dependent characteristic of the polarisation switching processes induced in the materials. A non-convex Helmholtz free energy based on Landau theory is proposed to model the switching dynamics. The governing equation of single-crystal model is formulated by applying the Euler-Lagrange equation. The polycrystalline model is obtained by combining the single crystal dynamics with a density function which is constructed to model the weighted contributions of different grains with different principle axis orientations. In addition, numerical simulations of hysteretic dynamics with creep phenomenon are presented. Comparison of the numerical results and their experimental counterparts is also presented. It is shown that the creep phenomenon is captured precisely, validating the capability of the proposed model in a range of its potential applications.

Integrating macro and micro scale approaches in the agent-based modeling of residential dynamics

NASA Astrophysics Data System (ADS)

Saeedi, Sara

2018-06-01

With the advancement of computational modeling and simulation (M&S) methods as well as data collection technologies, urban dynamics modeling substantially improved over the last several decades. The complex urban dynamics processes are most effectively modeled not at the macro-scale, but following a bottom-up approach, by simulating the decisions of individual entities, or residents. Agent-based modeling (ABM) provides the key to a dynamic M&S framework that is able to integrate socioeconomic with environmental models, and to operate at both micro and macro geographical scales. In this study, a multi-agent system is proposed to simulate residential dynamics by considering spatiotemporal land use changes. In the proposed ABM, macro-scale land use change prediction is modeled by Artificial Neural Network (ANN) and deployed as the agent environment and micro-scale residential dynamics behaviors autonomously implemented by household agents. These two levels of simulation interacted and jointly promoted urbanization process in an urban area of Tehran city in Iran. The model simulates the behavior of individual households in finding ideal locations to dwell. The household agents are divided into three main groups based on their income rank and they are further classified into different categories based on a number of attributes. These attributes determine the households' preferences for finding new dwellings and change with time. The ABM environment is represented by a land-use map in which the properties of the land parcels change dynamically over the simulation time. The outputs of this model are a set of maps showing the pattern of different groups of households in the city. These patterns can be used by city planners to find optimum locations for building new residential units or adding new services to the city. The simulation results show that combining macro- and micro-level simulation can give full play to the potential of the ABM to understand the driving mechanism of urbanization and provide decision-making support for urban management.

Evaluation of multidensity orthotic materials used in footwear for patients with diabetes.

PubMed

Foto, J G; Birke, J A

1998-12-01

Selected combinations of multidensity orthotic materials were tested under simulated walking conditions found in the forefoot of diabetic patients. Materials were compared for therapeutic effectiveness by their stress/strain properties and dynamic compression set. Results showed that all of the multidensity materials experienced losses in performance throughout the testing period of 100,000 cycles, with the greatest losses occurring within the first 10,000 cycles. Of the materials tested, Poron + Plastazote #2 and Spenco + Microcel Puff Lite had the highest dynamic material strain and the lowest dynamic compression set over 100,000 cycles. In comparison, these are better multidensity combinations than the others tested to use as therapeutic orthoses in footwear for diabetic patients.

A new method for the prediction of chatter stability lobes based on dynamic cutting force simulation model and support vector machine

NASA Astrophysics Data System (ADS)

Peng, Chong; Wang, Lun; Liao, T. Warren

2015-10-01

Currently, chatter has become the critical factor in hindering machining quality and productivity in machining processes. To avoid cutting chatter, a new method based on dynamic cutting force simulation model and support vector machine (SVM) is presented for the prediction of chatter stability lobes. The cutting force is selected as the monitoring signal, and the wavelet energy entropy theory is used to extract the feature vectors. A support vector machine is constructed using the MATLAB LIBSVM toolbox for pattern classification based on the feature vectors derived from the experimental cutting data. Then combining with the dynamic cutting force simulation model, the stability lobes diagram (SLD) can be estimated. Finally, the predicted results are compared with existing methods such as zero-order analytical (ZOA) and semi-discretization (SD) method as well as actual cutting experimental results to confirm the validity of this new method.

Self-organization in suspensions of end-functionalized semiflexible polymers under shear flow

NASA Astrophysics Data System (ADS)

Myung, Jin Suk; Winkler, Roland G.; Gompper, Gerhard

2015-12-01

The nonequilibrium dynamical behavior and structure formation of end-functionalized semiflexible polymer suspensions under flow are investigated by mesoscale hydrodynamic simulations. The hybrid simulation approach combines the multiparticle collision dynamics method for the fluid, which accounts for hydrodynamic interactions, with molecular dynamics simulations for the semiflexible polymers. In equilibrium, various kinds of scaffold-like network structures are observed, depending on polymer flexibility and end-attraction strength. We investigate the flow behavior of the polymer networks under shear and analyze their nonequilibrium structural and rheological properties. The scaffold structure breaks up and densified aggregates are formed at low shear rates, while the structural integrity is completely lost at high shear rates. We provide a detailed analysis of the shear- rate-dependent flow-induced structures. The studies provide a deeper understanding of the formation and deformation of network structures in complex materials.

Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations.

PubMed

Blöchliger, Nicolas; Caflisch, Amedeo; Vitalis, Andreas

2015-11-10

Data mining techniques depend strongly on how the data are represented and how distance between samples is measured. High-dimensional data often contain a large number of irrelevant dimensions (features) for a given query. These features act as noise and obfuscate relevant information. Unsupervised approaches to mine such data require distance measures that can account for feature relevance. Molecular dynamics simulations produce high-dimensional data sets describing molecules observed in time. Here, we propose to globally or locally weight simulation features based on effective rates. This emphasizes, in a data-driven manner, slow degrees of freedom that often report on the metastable states sampled by the molecular system. We couple this idea to several unsupervised learning protocols. Our approach unmasks slow side chain dynamics within the native state of a miniprotein and reveals additional metastable conformations of a protein. The approach can be combined with most algorithms for clustering or dimensionality reduction.

Ion-Molecule Reaction Dynamics

NASA Astrophysics Data System (ADS)

Meyer, Jennifer; Wester, Roland

2017-05-01

We review the recent advances in the investigation of the dynamics of ion-molecule reactions. During the past decade, the combination of single-collision experiments in crossed ion and neutral beams with the velocity map ion imaging detection technique has enabled a wealth of studies on ion-molecule reactions. These methods, in combination with chemical dynamics simulations, have uncovered new and unexpected reaction mechanisms, such as the roundabout mechanism and the subtle influence of the leaving group in anion-molecule nucleophilic substitution reactions. For this important class of reactions, as well as for many fundamental cation-molecule reactions, the information obtained with crossed-beam imaging is discussed. The first steps toward understanding micro-solvation of ion-molecule reaction dynamics are presented. We conclude with the presentation of several interesting directions for future research.

Dynamic Tunnel Usability Study: Format Recommendations for Synthetic Vision System Primary Flight Displays

NASA Technical Reports Server (NTRS)

Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Kramer, Lynda J.; Bailey, Randall E.

2006-01-01

A usability study evaluating dynamic tunnel concepts has been completed under the Aviation Safety and Security Program, Synthetic Vision Systems Project. The usability study was conducted in the Visual Imaging Simulator for Transport Aircraft Systems (VISTAS) III simulator in the form of questionnaires and pilot-in-the-loop simulation sessions. Twelve commercial pilots participated in the study to determine their preferences via paired comparisons and subjective rankings regarding the color, line thickness and sensitivity of the dynamic tunnel. The results of the study showed that color was not significant in pilot preference paired comparisons or in pilot rankings. Line thickness was significant for both pilot preference paired comparisons and in pilot rankings. The preferred line/halo thickness combination was a line width of 3 pixels and a halo of 4 pixels. Finally, pilots were asked their preference for the current dynamic tunnel compared to a less sensitive dynamic tunnel. The current dynamic tunnel constantly gives feedback to the pilot with regard to path error while the less sensitive tunnel only changes as the path error approaches the edges of the tunnel. The tunnel sensitivity comparison results were not statistically significant.

Reaching extended length-scales with accelerated dynamics

NASA Astrophysics Data System (ADS)

Hubartt, Bradley; Shim, Yunsic; Amar, Jacques

2012-02-01

While temperature-accelerated dynamics (TAD) has been quite successful in extending the time-scales for non-equilibrium simulations of small systems, the computational time increases rapidly with system size. One possible solution to this problem, which we refer to as parTAD^1 is to use spatial decomposition combined with our previously developed semi-rigorous synchronous sublattice algorithm^2. However, while such an approach leads to significantly better scaling as a function of system-size, it also artificially limits the size of activated events and is not completely rigorous. Here we discuss progress we have made in developing an alternative approach in which localized saddle-point searches are combined with parallel GPU-based molecular dynamics in order to improve the scaling behavior. By using this method, along with the use of an adaptive method to determine the optimal high-temperature^3, we have been able to significantly increase the range of time- and length-scales over which accelerated dynamics simulations may be carried out. [1] Y. Shim et al, Phys. Rev. B 76, 205439 (2007); ibid, Phys. Rev. Lett. 101, 116101 (2008). [2] Y. Shim and J.G. Amar, Phys. Rev. B 71, 125432 (2005). [3] Y. Shim and J.G. Amar, J. Chem. Phys. 134, 054127 (2011).

Optimisation potential for a SBR plant based upon integrated modelling for dry and wet weather conditions.

PubMed

Rönner-Holm, S G E; Kaufmann Alves, I; Steinmetz, H; Holm, N C

2009-01-01

Integrated dynamic simulation analysis of a full-scale municipal sequential batch reactor (SBR) wastewater treatment plant (WWTP) was performed using the KOSMO pollution load simulation model for the combined sewer system (CSS) and the ASM3 + EAWAG-BioP model for the WWTP. Various optimising strategies for dry and storm weather conditions were developed to raise the purification and hydraulic performance and to reduce operation costs based on simulation studies with the calibrated WWTP model. The implementation of some strategies on the plant led to lower effluent values and an average annual saving of 49,000 euro including sewage tax, which is 22% of the total running costs. Dynamic simulation analysis of CSS for an increased WWTP influent over a period of one year showed high potentials for reducing combined sewer overflow (CSO) volume by 18-27% and CSO loads for COD by 22%, NH(4)-N and P(total) by 33%. In addition, the SBR WWTP could easily handle much higher influents without exceeding the monitoring values. During the integrated simulation of representative storm events, the total emission load for COD dropped to 90%, the sewer system emitted 47% less, whereas the pollution load in the WWTP effluent increased to only 14% with 2% higher running costs.

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

PubMed Central

Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D.; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll.

2016-01-01

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. PMID:26612862

Influence of feedbacks from simulated crop growth on integrated regional hydrologic simulations under climate scenarios

NASA Astrophysics Data System (ADS)

van Walsum, P. E. V.

2011-11-01

Climate change impact modelling of hydrologic responses is hampered by climate-dependent model parameterizations. Reducing this dependency was one of the goals of extending the regional hydrologic modelling system SIMGRO with a two-way coupling to the crop growth simulation model WOFOST. The coupling includes feedbacks to the hydrologic model in terms of the root zone depth, soil cover, leaf area index, interception storage capacity, crop height and crop factor. For investigating whether such feedbacks lead to significantly different simulation results, two versions of the model coupling were set up for a test region: one with exogenous vegetation parameters, the "static" model, and one with endogenous simulation of the crop growth, the "dynamic" model WOFOST. The used parameterization methods of the static/dynamic vegetation models ensure that for the current climate the simulated long-term average of the actual evapotranspiration is the same for both models. Simulations were made for two climate scenarios. Owing to the higher temperatures in combination with a higher CO2-concentration of the atmosphere, a forward time shift of the crop development is simulated in the dynamic model; the used arable land crop, potatoes, also shows a shortening of the growing season. For this crop, a significant reduction of the potential transpiration is simulated compared to the static model, in the example by 15% in a warm, dry year. In consequence, the simulated crop water stress (the unit minus the relative transpiration) is lower when the dynamic model is used; also the simulated increase of crop water stress due to climate change is lower; in the example, the simulated increase is 15 percentage points less (of 55) than when a static model is used. The static/dynamic models also simulate different absolute values of the transpiration. The difference is most pronounced for potatoes at locations with ample moisture supply; this supply can either come from storage release of a good soil or from capillary rise. With good supply of moisture, the dynamic model simulates up to 10% less actual evapotranspiration than the static one in the example. This can lead to cases where the dynamic model predicts a slight increase of the recharge in a climate scenario, where the static model predicts a decrease. The use of a dynamic model also affects the simulated demand for surface water from external sources; especially the timing is affected. The proposed modelling approach uses postulated relationships that require validation with controlled field trials. In the Netherlands there is a lack of experimental facilities for performing such validations.

Modeling universal dynamics of cell spreading on elastic substrates.

PubMed

Fan, Houfu; Li, Shaofan

2015-11-01

A three-dimensional (3D) multiscale moving contact line model is combined with a soft matter cell model to study the universal dynamics of cell spreading over elastic substrates. We have studied both the early stage and the late stage cell spreading by taking into account the actin tension effect. In this work, the cell is modeled as an active nematic droplet, and the substrate is modeled as a St. Venant Kirchhoff elastic medium. A complete 3D simulation of cell spreading has been carried out. The simulation results show that the spreading area versus spreading time at different stages obeys specific power laws, which is in good agreement with experimental data and theoretical prediction reported in the literature. Moreover, the simulation results show that the substrate elasticity may affect force dipole distribution inside the cell. The advantage of this approach is that it combines the hydrodynamics of actin retrograde flow with moving contact line model so that it can naturally include actin tension effect resulting from actin polymerization and actomyosin contraction, and thus it might be capable of simulating complex cellular scale phenomenon, such as cell spreading or even crawling.

All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

PubMed

Prior, C; Danilāne, L; Oganesyan, V S

2018-05-16

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

Calibration and validation of a spar-type floating offshore wind turbine model using the FAST dynamic simulation tool

DOE PAGES

Browning, J. R.; Jonkman, J.; Robertson, A.; ...

2014-12-16

In this study, high-quality computer simulations are required when designing floating wind turbines because of the complex dynamic responses that are inherent with a high number of degrees of freedom and variable metocean conditions. In 2007, the FAST wind turbine simulation tool, developed and maintained by the U.S. Department of Energy's (DOE's) National Renewable Energy Laboratory (NREL), was expanded to include capabilities that are suitable for modeling floating offshore wind turbines. In an effort to validate FAST and other offshore wind energy modeling tools, DOE funded the DeepCwind project that tested three prototype floating wind turbines at 1/50 th scalemore » in a wave basin, including a semisubmersible, a tension-leg platform, and a spar buoy. This paper describes the use of the results of the spar wave basin tests to calibrate and validate the FAST offshore floating simulation tool, and presents some initial results of simulated dynamic responses of the spar to several combinations of wind and sea states. Wave basin tests with the spar attached to a scale model of the NREL 5-megawatt reference wind turbine were performed at the Maritime Research Institute Netherlands under the DeepCwind project. This project included free-decay tests, tests with steady or turbulent wind and still water (both periodic and irregular waves with no wind), and combined wind/wave tests. The resulting data from the 1/50th model was scaled using Froude scaling to full size and used to calibrate and validate a full-size simulated model in FAST. Results of the model calibration and validation include successes, subtleties, and limitations of both wave basin testing and FAST modeling capabilities.« less

Exploring an Ecologically Sustainable Scheme for Landscape Restoration of Abandoned Mine Land: Scenario-Based Simulation Integrated Linear Programming and CLUE-S Model

PubMed Central

Zhang, Liping; Zhang, Shiwen; Huang, Yajie; Cao, Meng; Huang, Yuanfang; Zhang, Hongyan

2016-01-01

Understanding abandoned mine land (AML) changes during land reclamation is crucial for reusing damaged land resources and formulating sound ecological restoration policies. This study combines the linear programming (LP) model and the CLUE-S model to simulate land-use dynamics in the Mentougou District (Beijing, China) from 2007 to 2020 under three reclamation scenarios, that is, the planning scenario based on the general land-use plan in study area (scenario 1), maximal comprehensive benefits (scenario 2), and maximal ecosystem service value (scenario 3). Nine landscape-scale graph metrics were then selected to describe the landscape characteristics. The results show that the coupled model presented can simulate the dynamics of AML effectively and the spatially explicit transformations of AML were different. New cultivated land dominates in scenario 1, while construction land and forest land account for major percentages in scenarios 2 and 3, respectively. Scenario 3 has an advantage in most of the selected indices as the patches combined most closely. To conclude, reclaiming AML by transformation into more forest can reduce the variability and maintain the stability of the landscape ecological system in study area. These findings contribute to better mapping AML dynamics and providing policy support for the management of AML. PMID:27023575

A compartment model of alveolar-capillary oxygen diffusion with ventilation-perfusion gradient and dynamics of air transport through the respiratory tract.

PubMed

Jaworski, Jacek; Redlarski, Grzegorz

2014-08-01

This paper presents a model of alveolar-capillary oxygen diffusion with dynamics of air transport through the respiratory tract. For this purpose electrical model representing the respiratory tract mechanics and differential equations representing oxygen membrane diffusion are combined. Relevant thermodynamic relations describing the mass of oxygen transported into the human body are proposed as the connection between these models, as well as the influence of ventilation-perfusion mismatch on the oxygen diffusion. The model is verified based on simulation results of varying exercise intensities and statistical calculations of the results obtained during various clinical trials. The benefit of the approach proposed is its application in simulation-based research aimed to generate quantitative data of normal and pathological conditions. Based on the model presented, taking into account many essential physiological processes and air transport dynamics, comprehensive and combined studies of the respiratory efficiency can be performed. The impact of physical exercise, precise changes in respiratory tract mechanics and alterations in breathing pattern can be analyzed together with the impact of various changes in alveolar-capillary oxygen diffusion. This may be useful in simulation of effects of many severe medical conditions and increased activity level. Copyright © 2014 Elsevier Ltd. All rights reserved.

Exploring an Ecologically Sustainable Scheme for Landscape Restoration of Abandoned Mine Land: Scenario-Based Simulation Integrated Linear Programming and CLUE-S Model.

PubMed

Zhang, Liping; Zhang, Shiwen; Huang, Yajie; Cao, Meng; Huang, Yuanfang; Zhang, Hongyan

2016-03-24

Understanding abandoned mine land (AML) changes during land reclamation is crucial for reusing damaged land resources and formulating sound ecological restoration policies. This study combines the linear programming (LP) model and the CLUE-S model to simulate land-use dynamics in the Mentougou District (Beijing, China) from 2007 to 2020 under three reclamation scenarios, that is, the planning scenario based on the general land-use plan in study area (scenario 1), maximal comprehensive benefits (scenario 2), and maximal ecosystem service value (scenario 3). Nine landscape-scale graph metrics were then selected to describe the landscape characteristics. The results show that the coupled model presented can simulate the dynamics of AML effectively and the spatially explicit transformations of AML were different. New cultivated land dominates in scenario 1, while construction land and forest land account for major percentages in scenarios 2 and 3, respectively. Scenario 3 has an advantage in most of the selected indices as the patches combined most closely. To conclude, reclaiming AML by transformation into more forest can reduce the variability and maintain the stability of the landscape ecological system in study area. These findings contribute to better mapping AML dynamics and providing policy support for the management of AML.

Controlling protein molecular dynamics: How to accelerate folding while preserving the native state

NASA Astrophysics Data System (ADS)

Jensen, Christian H.; Nerukh, Dmitry; Glen, Robert C.

2008-12-01

The dynamics of peptides and proteins generated by classical molecular dynamics (MD) is described by using a Markov model. The model is built by clustering the trajectory into conformational states and estimating transition probabilities between the states. Assuming that it is possible to influence the dynamics of the system by varying simulation parameters, we show how to use the Markov model to determine the parameter values that preserve the folded state of the protein and at the same time, reduce the folding time in the simulation. We investigate this by applying the method to two systems. The first system is an imaginary peptide described by given transition probabilities with a total folding time of 1μs. We find that only small changes in the transition probabilities are needed to accelerate (or decelerate) the folding. This implies that folding times for slowly folding peptides and proteins calculated using MD cannot be meaningfully compared to experimental results. The second system is a four residue peptide valine-proline-alanine-leucine in water. We control the dynamics of the transitions by varying the temperature and the atom masses. The simulation results show that it is possible to find the combinations of parameter values that accelerate the dynamics and at the same time preserve the native state of the peptide. A method for accelerating larger systems without performing simulations for the whole folding process is outlined.

Modeling of Stick-Slip Behavior in Sheared Granular Fault Gouge Using the Combined Finite-Discrete Element Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Ke; Euser, Bryan J.; Rougier, Esteban

Sheared granular layers undergoing stick-slip behavior are broadly employed to study the physics and dynamics of earthquakes. In this paper, a two-dimensional implementation of the combined finite-discrete element method (FDEM), which merges the finite element method (FEM) and the discrete element method (DEM), is used to explicitly simulate a sheared granular fault system including both gouge and plate, and to investigate the influence of different normal loads on seismic moment, macroscopic friction coefficient, kinetic energy, gouge layer thickness, and recurrence time between slips. In the FDEM model, the deformation of plates and particles is simulated using the FEM formulation whilemore » particle-particle and particle-plate interactions are modeled using DEM-derived techniques. The simulated seismic moment distributions are generally consistent with those obtained from the laboratory experiments. In addition, the simulation results demonstrate that with increasing normal load, (i) the kinetic energy of the granular fault system increases; (ii) the gouge layer thickness shows a decreasing trend; and (iii) the macroscopic friction coefficient does not experience much change. Analyses of the slip events reveal that, as the normal load increases, more slip events with large kinetic energy release and longer recurrence time occur, and the magnitude of gouge layer thickness decrease also tends to be larger; while the macroscopic friction coefficient drop decreases. Finally, the simulations not only reveal the influence of normal loads on the dynamics of sheared granular fault gouge, but also demonstrate the capabilities of FDEM for studying stick-slip dynamic behavior of granular fault systems.« less

Modeling of Stick-Slip Behavior in Sheared Granular Fault Gouge Using the Combined Finite-Discrete Element Method

DOE PAGES

Gao, Ke; Euser, Bryan J.; Rougier, Esteban; ...

2018-06-20

Sheared granular layers undergoing stick-slip behavior are broadly employed to study the physics and dynamics of earthquakes. In this paper, a two-dimensional implementation of the combined finite-discrete element method (FDEM), which merges the finite element method (FEM) and the discrete element method (DEM), is used to explicitly simulate a sheared granular fault system including both gouge and plate, and to investigate the influence of different normal loads on seismic moment, macroscopic friction coefficient, kinetic energy, gouge layer thickness, and recurrence time between slips. In the FDEM model, the deformation of plates and particles is simulated using the FEM formulation whilemore » particle-particle and particle-plate interactions are modeled using DEM-derived techniques. The simulated seismic moment distributions are generally consistent with those obtained from the laboratory experiments. In addition, the simulation results demonstrate that with increasing normal load, (i) the kinetic energy of the granular fault system increases; (ii) the gouge layer thickness shows a decreasing trend; and (iii) the macroscopic friction coefficient does not experience much change. Analyses of the slip events reveal that, as the normal load increases, more slip events with large kinetic energy release and longer recurrence time occur, and the magnitude of gouge layer thickness decrease also tends to be larger; while the macroscopic friction coefficient drop decreases. Finally, the simulations not only reveal the influence of normal loads on the dynamics of sheared granular fault gouge, but also demonstrate the capabilities of FDEM for studying stick-slip dynamic behavior of granular fault systems.« less

Molecular dynamics simulation of liquid structure for undercooled Zr-Nb alloys assisted with electrostatic levitation experiments

NASA Astrophysics Data System (ADS)

Yang, S. J.; Hu, L.; Wang, L.; Wei, B.

2018-06-01

The liquid structures of undercooled Zr90Nb10, Zr70Nb30 and Zr50Nb50 alloys were studied by molecular dynamics simulation combined with electrostatic levitation experiments. The densities of three alloys were measured by electrostatic levitation to modify the Zr-Nb potential functions by adjusting parameters in potential functions. In simulation, the atomic packing in Zr-Nb alloys was more ordered at lower temperatures. The Voronoi tessellation analyses indicated Nb-centered clusters were easier to form than Zr-centered clusters although the Nb content was less than 50%. The partial pair distribution functions showed that the interactions among Zr atoms are quite different to that among Nb atoms.

An Empirical Study of Combining Communicating Processes in a Parallel Discrete Event Simulation

DTIC Science & Technology

1990-12-01

dynamics of the cost/performance criteria which typically made up computer resource acquisition decisions . offering a broad range of tradeoffs in the way... prcesses has a significant impact on simulation performance. It is the hypothesis of this 3-4 SYSTEM DECOMPOSITION PHYSICAL SYSTEM 1: N PHYSICAL PROCESS 1...EMPTY)) next-event = pop(next-event-queue); lp-clock = next-event - time; Simulate next event departure- consume event-enqueue new event end while; If no

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

PubMed Central

Boldon, Lauren; Laliberte, Fallon; Liu, Li

2015-01-01

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques. PMID:25721341

Uniaxial ratchetting of 316FR steel at room temperature -- Part 2. Constitutive modeling and simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohno, N.; Abdel-Karim, M.

2000-01-01

Uniaxial ratchetting experiments of 316FR steel at room temperature reported in Part 1 are simulated using a new kinematic hardening model which has two kinds of dynamic recovery terms. The model, which features the capability of simulating slight opening of stress-strain hysteresis loops robustly, is formulated by furnishing the Armstrong and Frederick model with the critical state of dynamic recovery introduced by Ohno and Wang (1993). The model is then combined with a viscoplastic equation, and the resulting constitutive model is applied successfully to simulating the experiments. It is shown that for ratchetting under stress cycling with negative stress ratio,more » viscoplasticity and slight opening of hysteresis loops are effective mainly in early and subsequent cycles, respectively, whereas for ratchetting under zero-to-tension only viscoplasticity is effective.« less

Spectral solver for multi-scale plasma physics simulations with dynamically adaptive number of moments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vencels, Juris; Delzanno, Gian Luca; Johnson, Alec

2015-06-01

A spectral method for kinetic plasma simulations based on the expansion of the velocity distribution function in a variable number of Hermite polynomials is presented. The method is based on a set of non-linear equations that is solved to determine the coefficients of the Hermite expansion satisfying the Vlasov and Poisson equations. In this paper, we first show that this technique combines the fluid and kinetic approaches into one framework. Second, we present an adaptive strategy to increase and decrease the number of Hermite functions dynamically during the simulation. The technique is applied to the Landau damping and two-stream instabilitymore » test problems. Performance results show 21% and 47% saving of total simulation time in the Landau and two-stream instability test cases, respectively.« less

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

PubMed

Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

2015-10-01

It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

PubMed Central

Dijkstra, Maurits J. J.; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

2015-01-01

It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

Self-Consistent Determination of Atomic Charges of Ionic Liquid through a Combination of Molecular Dynamics Simulation and Density Functional Theory.

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2016-02-09

A self-consistent scheme is developed to determine the atomic partial charges of ionic liquid. Molecular dynamics (MD) simulation was conducted to sample a set of ion configurations, and these configurations were subject to density functional theory (DFT) calculations to determine the partial charges. The charges were then averaged and used as inputs for the subsequent MD simulation, and MD and DFT calculations were repeated until the MD results are not altered any more. We applied this scheme to 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ([C1mim][NTf2]) and investigated its structure and dynamics as a function of temperature. At convergence, the average ionic charges were ±0.84 e at 350 K due to charge transfer among ions, where e is the elementary charge, while the reduced ionic charges do not affect strongly the density of [C1mim][NTf2] and radial distribution function. Instead, major effects are found on the energetics and dynamics, with improvements of the overestimated heat of vaporization and the too slow motions of ions observed in MD simulations using commonly used force fields.

Integration of Continuous-Time Dynamics in a Spiking Neural Network Simulator.

PubMed

Hahne, Jan; Dahmen, David; Schuecker, Jannis; Frommer, Andreas; Bolten, Matthias; Helias, Moritz; Diesmann, Markus

2017-01-01

Contemporary modeling approaches to the dynamics of neural networks include two important classes of models: biologically grounded spiking neuron models and functionally inspired rate-based units. We present a unified simulation framework that supports the combination of the two for multi-scale modeling, enables the quantitative validation of mean-field approaches by spiking network simulations, and provides an increase in reliability by usage of the same simulation code and the same network model specifications for both model classes. While most spiking simulations rely on the communication of discrete events, rate models require time-continuous interactions between neurons. Exploiting the conceptual similarity to the inclusion of gap junctions in spiking network simulations, we arrive at a reference implementation of instantaneous and delayed interactions between rate-based models in a spiking network simulator. The separation of rate dynamics from the general connection and communication infrastructure ensures flexibility of the framework. In addition to the standard implementation we present an iterative approach based on waveform-relaxation techniques to reduce communication and increase performance for large-scale simulations of rate-based models with instantaneous interactions. Finally we demonstrate the broad applicability of the framework by considering various examples from the literature, ranging from random networks to neural-field models. The study provides the prerequisite for interactions between rate-based and spiking models in a joint simulation.

Integration of Continuous-Time Dynamics in a Spiking Neural Network Simulator

PubMed Central

Hahne, Jan; Dahmen, David; Schuecker, Jannis; Frommer, Andreas; Bolten, Matthias; Helias, Moritz; Diesmann, Markus

2017-01-01

Contemporary modeling approaches to the dynamics of neural networks include two important classes of models: biologically grounded spiking neuron models and functionally inspired rate-based units. We present a unified simulation framework that supports the combination of the two for multi-scale modeling, enables the quantitative validation of mean-field approaches by spiking network simulations, and provides an increase in reliability by usage of the same simulation code and the same network model specifications for both model classes. While most spiking simulations rely on the communication of discrete events, rate models require time-continuous interactions between neurons. Exploiting the conceptual similarity to the inclusion of gap junctions in spiking network simulations, we arrive at a reference implementation of instantaneous and delayed interactions between rate-based models in a spiking network simulator. The separation of rate dynamics from the general connection and communication infrastructure ensures flexibility of the framework. In addition to the standard implementation we present an iterative approach based on waveform-relaxation techniques to reduce communication and increase performance for large-scale simulations of rate-based models with instantaneous interactions. Finally we demonstrate the broad applicability of the framework by considering various examples from the literature, ranging from random networks to neural-field models. The study provides the prerequisite for interactions between rate-based and spiking models in a joint simulation. PMID:28596730

An Integrated Approach to Modeling Solar Electric Propulsion Vehicles During Long Duration, Near-Earth Orbit Transfers

NASA Technical Reports Server (NTRS)

Smith, David A.; Hojnicki, Jeffrey S.; Sjauw, Waldy K.

2014-01-01

Recent NASA interest in utilizing solar electronic propulsion (SEP) technology to transfer payloads, e.g. from low-Earth orbit (LEO) to higher energy geostationary-Earth orbit (GEO) or to Earth escape, has necessitated the development of high fidelity SEP vehicle models and simulations. These models and simulations need to be capable of capturing vehicle dynamics and sub-system interactions experienced during the transfer trajectories which are typically accomplished with continuous-burn (potentially interrupted by solar eclipse), long duration "spiral out" maneuvers taking several months or more to complete. This paper presents details of an integrated simulation approach achieved by combining a high fidelity vehicle simulation code with a detailed solar array model. The combined simulation tool gives researchers the functionality to study the integrated effects of various vehicle sub-systems (e.g. vehicle guidance, navigation and control (GN&C), electric propulsion system (EP)) with time varying power production. Results from a simulation model of a vehicle with a 50 kW class SEP system using the integrated tool are presented and compared to the results from another simulation model employing a 50 kW end-of-life (EOL) fixed power level assumption. These models simulate a vehicle under three degree of freedom dynamics (i.e. translational dynamics only) and include the effects of a targeting guidance algorithm (providing a "near optimal" transfer) during a LEO to near Earth escape (C (sub 3) = -2.0 km (sup 2) / sec (sup -2) spiral trajectory. The presented results include the impact of the fully integrated, time-varying solar array model (e.g. cumulative array degradation from traversing the Van Allen belts, impact of solar eclipses on the vehicle and the related temperature responses in the solar arrays due to operating in the Earth's thermal environment, high fidelity array power module, etc.); these are used to assess the impact on vehicle performance (i.e. propellant consumption) and transit times.

Atomistic modeling of La 3+ doping segregation effect on nanocrystalline yttria-stabilized zirconia

DOE PAGES

Zhang, Shenli; Sha, Haoyan; Castro, Ricardo H. R.; ...

2018-01-01

The effect of La 3+ doping on the structure and ionic conductivity change in nanocrystalline yttria-stabilized zirconia (YSZ) was studied using a combination of Monte Carlo and molecular dynamics simulations.

Exploring the folding pattern of a polymer chain in a single crystal by combining single-molecule force spectroscopy and steered molecular dynamics simulations.

PubMed

Song, Yu; Feng, Wei; Liu, Kai; Yang, Peng; Zhang, Wenke; Zhang, Xi

2013-03-26

Understanding the folding pattern of a single polymer chain within its single crystal will shed light on the mechanism of crystallization. Here, we use the combined techniques of atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations to study the folding pattern of a polyethylene oxide (PEO) chain in its single crystal. Our results show that the folding pattern of a PEO chain in the crystal formed in dilute solution follows the adjacent re-entry folding model. While in the crystal obtained from the melt, the nonadjacent folding with large and irregular loops contributes to big force fluctuations in the force-extension curves. The method established here can offer a novel strategy to directly unravel the chain-folding pattern of polymer single crystals at single-molecule level.

Role of small oligomers on the amyloidogenic aggregation free-energy landscape.

PubMed

He, Xianglan; Giurleo, Jason T; Talaga, David S

2010-01-08

We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of beta-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.

Energy evaluation of protection effectiveness of anti-vibration gloves.

PubMed

Hermann, Tomasz; Dobry, Marian Witalis

2017-09-01

This article describes an energy method of assessing protection effectiveness of anti-vibration gloves on the human dynamic structure. The study uses dynamic models of the human and the glove specified in Standard No. ISO 10068:2012. The physical models of human-tool systems were developed by combining human physical models with a power tool model. The combined human-tool models were then transformed into mathematical models from which energy models were finally derived. Comparative energy analysis was conducted in the domain of rms powers. The energy models of the human-tool systems were solved using numerical simulation implemented in the MATLAB/Simulink environment. The simulation procedure demonstrated the effectiveness of the anti-vibration glove as a method of protecting human operators of hand-held power tools against vibration. The desirable effect is achieved by lowering the flow of energy in the human-tool system when the anti-vibration glove is employed.

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

PubMed

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-07-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

Function and dynamics of aptamers: A case study on the malachite green aptamer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Tianjiao

Aptamers are short single-stranded nucleic acids that can bind to their targets with high specificity and high affinity. To study aptamer function and dynamics, the malachite green aptamer was chosen as a model. Malachite green (MG) bleaching, in which an OH- attacks the central carbon (C1) of MG, was inhibited in the presence of the malachite green aptamer (MGA). The inhibition of MG bleaching by MGA could be reversed by an antisense oligonucleotide (AS) complementary to the MGA binding pocket. Computational cavity analysis of the NMR structure of the MGA-MG complex predicted that the OH - is sterically excluded frommore » the C1 of MG. The prediction was confirmed experimentally using variants of the MGA with changes in the MG binding pocket. This work shows that molecular reactivity can be reversibly regulated by an aptamer-AS pair based on steric hindrance. In addition to demonstrate that aptamers could control molecular reactivity, aptamer dynamics was studied with a strategy combining molecular dynamics (MD) simulation and experimental verification. MD simulation predicted that the MG binding pocket of the MGA is largely pre-organized and that binding of MG involves reorganization of the pocket and a simultaneous twisting of the MGA terminal stems around the pocket. MD simulation also provided a 3D-structure model of unoccupied MGA that has not yet been obtained by biophysical measurements. These predictions were consistent with biochemical and biophysical measurements of the MGA-MG interaction including RNase I footprinting, melting curves, thermodynamic and kinetic constants measurement. This work shows that MD simulation can be used to extend our understanding of the dynamics of aptamer-target interaction which is not evident from static 3D-structures. To conclude, I have developed a novel concept to control molecular reactivity by an aptamer based on steric protection and a strategy to study the dynamics of aptamer-target interaction by combining MD simulation and experimental verification. The former has potential application in controlling metabolic reactions and protein modifications by small reactants and the latter may serve as a general approach to study the dynamics of aptamer-target interaction for new insights into mechanisms of aptamer-target recognition.« less

Simulation of land use change in the three gorges reservoir area based on CART-CA

NASA Astrophysics Data System (ADS)

Yuan, Min

2018-05-01

This study proposes a new method to simulate spatiotemporal complex multiple land uses by using classification and regression tree algorithm (CART) based CA model. In this model, we use classification and regression tree algorithm to calculate land class conversion probability, and combine neighborhood factor, random factor to extract cellular transformation rules. The overall Kappa coefficient is 0.8014 and the overall accuracy is 0.8821 in the land dynamic simulation results of the three gorges reservoir area from 2000 to 2010, and the simulation results are satisfactory.

Inlet Development for a Rocket Based Combined Cycle, Single Stage to Orbit Vehicle Using Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

DeBonis, J. R.; Trefny, C. J.; Steffen, C. J., Jr.

1999-01-01

Design and analysis of the inlet for a rocket based combined cycle engine is discussed. Computational fluid dynamics was used in both the design and subsequent analysis. Reynolds averaged Navier-Stokes simulations were performed using both perfect gas and real gas assumptions. An inlet design that operates over the required Mach number range from 0 to 12 was produced. Performance data for cycle analysis was post processed using a stream thrust averaging technique. A detailed performance database for cycle analysis is presented. The effect ot vehicle forebody compression on air capture is also examined.

Exact subthreshold integration with continuous spike times in discrete-time neural network simulations.

PubMed

Morrison, Abigail; Straube, Sirko; Plesser, Hans Ekkehard; Diesmann, Markus

2007-01-01

Very large networks of spiking neurons can be simulated efficiently in parallel under the constraint that spike times are bound to an equidistant time grid. Within this scheme, the subthreshold dynamics of a wide class of integrate-and-fire-type neuron models can be integrated exactly from one grid point to the next. However, the loss in accuracy caused by restricting spike times to the grid can have undesirable consequences, which has led to interest in interpolating spike times between the grid points to retrieve an adequate representation of network dynamics. We demonstrate that the exact integration scheme can be combined naturally with off-grid spike events found by interpolation. We show that by exploiting the existence of a minimal synaptic propagation delay, the need for a central event queue is removed, so that the precision of event-driven simulation on the level of single neurons is combined with the efficiency of time-driven global scheduling. Further, for neuron models with linear subthreshold dynamics, even local event queuing can be avoided, resulting in much greater efficiency on the single-neuron level. These ideas are exemplified by two implementations of a widely used neuron model. We present a measure for the efficiency of network simulations in terms of their integration error and show that for a wide range of input spike rates, the novel techniques we present are both more accurate and faster than standard techniques.

Dispersal responses override density effects on genetic diversity during post-disturbance succession

PubMed Central

Landguth, Erin L.; Bull, C. Michael; Banks, Sam C.; Gardner, Michael G.; Driscoll, Don A.

2016-01-01

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus. We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity in N. stellatus. Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics. PMID:27009225

Exploring the limits of knowledge on boreal peatland development using a new model: the Holocene Peatland Model

NASA Astrophysics Data System (ADS)

Quillet, Anne; Garneau, Michelle; Frolking, Steve; Roulet, Nigel; Peng, Changhui

2010-05-01

The Holocene Peatland Model (HPM) (Frolking et al. 2009, Frolking et al. in prep.) is a recently developed tool integrating up-to-date knowledge on peatland dynamics that explores peatland development and carbon dynamics on a millennial timescale. HPM combines the water and carbon cycles with net primary production and peat decomposition and takes the multiple feedbacks into account. The model remains simple and few site-specific inputs are needed. HPM simulates the transient development of the peatland and delivers peat age, peat depth, peat composition, carbon accumulation and water table depth for each simulated year. Evaluating the ability of the model to reproduce peatland development can be achieved in several manners. Commonly one could choose to compare simulations results with observations from field data. However, we argue that the overall response of the model does not give much information about the value of the model design. Modelling of peatlands dynamics requires a lot of information regarding the behaviour of a peatland system within its environment (including allogenic changes in climate, hydrological conditions, nutrient availability or autogenic processes such as microtopographical effects). The actual state of knowledge does not cover all processes, interactions or feedbacks and a lot of peatland properties are neither well defined nor measured yet, so that estimates have been needed to build the model. The work presented here aims at analyzing the role of the model parameterization on the simulation results. To do so, a sensitivity analysis is performed with a Monte-Carlo analysis and with help of the GUI-HDMR software (Ziehn and Tomlin, 2009). This method ranks the parameters and combinations of them according to their influence on simulation results. The results will emphasize how the simulation is sensitive to the parameter values. First, the distribution of outputs gives insight into the possible responses of the simulation to HPM's assemblage of current knowledge. Second, the importance of some parameters on simulation results points out certain gaps in the current understanding of peatland dynamics. Thus, this study helps determine some avenues that should be explored in future in order to improve peatlands dynamics understanding. Frolking S, NT Roulet, A Quillet, E Tuittila, JL Bubier. 2009. Simulating long-term carbon and water dynamics in northern peatlands Eos Trans. AGU, 90(52), Fall Meet. Suppl., Abstract PP12B-05. Frolking S, NT Roulet, E Tuittila, JL Bubier, A Quillet. XXXX. A new model of Holocene peatland net primary production, decomposition, and peat accumulation. in prep. Ziehn T, AS Tomlin. 2009. GUI-HDMR - A solftware tool for global sensitivity analysis of complex models. Environmental Modelling & Software, 24, 775-785.

Primary combination of phase-field and discrete dislocation dynamics methods for investigating athermal plastic deformation in various realistic Ni-base single crystal superalloy microstructures

NASA Astrophysics Data System (ADS)

Gao, Siwen; Rajendran, Mohan Kumar; Fivel, Marc; Ma, Anxin; Shchyglo, Oleg; Hartmaier, Alexander; Steinbach, Ingo

2015-10-01

Three-dimensional discrete dislocation dynamics (DDD) simulations in combination with the phase-field method are performed to investigate the influence of different realistic Ni-base single crystal superalloy microstructures with the same volume fraction of {γ\\prime} precipitates on plastic deformation at room temperature. The phase-field method is used to generate realistic microstructures as the boundary conditions for DDD simulations in which a constant high uniaxial tensile load is applied along different crystallographic directions. In addition, the lattice mismatch between the γ and {γ\\prime} phases is taken into account as a source of internal stresses. Due to the high antiphase boundary energy and the rare formation of superdislocations, precipitate cutting is not observed in the present simulations. Therefore, the plastic deformation is mainly caused by dislocation motion in γ matrix channels. From a comparison of the macroscopic mechanical response and the dislocation evolution for different microstructures in each loading direction, we found that, for a given {γ\\prime} phase volume fraction, the optimal microstructure should possess narrow and homogeneous γ matrix channels.

Studies on the population dynamics of a rumor-spreading model in online social networks

NASA Astrophysics Data System (ADS)

Dong, Suyalatu; Fan, Feng-Hua; Huang, Yong-Chang

2018-02-01

This paper sets up a rumor spreading model in online social networks based on the European fox rabies SIR model. The model considers the impact of changing number of online social network users, combines the transmission dynamics to set up a population dynamics of rumor spreading model in online social networks. Simulation is carried out on online social network, and results show that the new rumor spreading model is in accordance with the real propagation characteristics in online social networks.

Quantum dynamics of thermalizing systems

NASA Astrophysics Data System (ADS)

White, Christopher David; Zaletel, Michael; Mong, Roger S. K.; Refael, Gil

2018-01-01

We introduce a method "DMT" for approximating density operators of 1D systems that, when combined with a standard framework for time evolution (TEBD), makes possible simulation of the dynamics of strongly thermalizing systems to arbitrary times. We demonstrate that the method performs well for both near-equilibrium initial states (Gibbs states with spatially varying temperatures) and far-from-equilibrium initial states, including quenches across phase transitions and pure states.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models.

PubMed

Li, Min; Zhang, John Z H

2017-02-14

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models

NASA Astrophysics Data System (ADS)

Li, Min; Zhang, John Z. H.

2017-02-01

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

An ice sheet model validation framework for the Greenland ice sheet.

PubMed

Price, Stephen F; Hoffman, Matthew J; Bonin, Jennifer A; Howat, Ian M; Neumann, Thomas; Saba, Jack; Tezaur, Irina; Guerber, Jeffrey; Chambers, Don P; Evans, Katherine J; Kennedy, Joseph H; Lenaerts, Jan; Lipscomb, William H; Perego, Mauro; Salinger, Andrew G; Tuminaro, Raymond S; van den Broeke, Michiel R; Nowicki, Sophie M J

2017-01-01

We propose a new ice sheet model validation framework - the Cryospheric Model Comparison Tool (CmCt) - that takes advantage of ice sheet altimetry and gravimetry observations collected over the past several decades and is applied here to modeling of the Greenland ice sheet. We use realistic simulations performed with the Community Ice Sheet Model (CISM) along with two idealized, non-dynamic models to demonstrate the framework and its use. Dynamic simulations with CISM are forced from 1991 to 2013 using combinations of reanalysis-based surface mass balance and observations of outlet glacier flux change. We propose and demonstrate qualitative and quantitative metrics for use in evaluating the different model simulations against the observations. We find that the altimetry observations used here are largely ambiguous in terms of their ability to distinguish one simulation from another. Based on basin- and whole-ice-sheet scale metrics, we find that simulations using both idealized conceptual models and dynamic, numerical models provide an equally reasonable representation of the ice sheet surface (mean elevation differences of <1 m). This is likely due to their short period of record, biases inherent to digital elevation models used for model initial conditions, and biases resulting from firn dynamics, which are not explicitly accounted for in the models or observations. On the other hand, we find that the gravimetry observations used here are able to unambiguously distinguish between simulations of varying complexity, and along with the CmCt, can provide a quantitative score for assessing a particular model and/or simulation. The new framework demonstrates that our proposed metrics can distinguish relatively better from relatively worse simulations and that dynamic ice sheet models, when appropriately initialized and forced with the right boundary conditions, demonstrate predictive skill with respect to observed dynamic changes occurring on Greenland over the past few decades. An extensible design will allow for continued use of the CmCt as future altimetry, gravimetry, and other remotely sensed data become available for use in ice sheet model validation.

Determination of detonation wave boundary angles via hydrocode simulations using CREST

NASA Astrophysics Data System (ADS)

Whitworth, N. J.; Childs, M.

2017-01-01

A key input parameter to Detonation Shock Dynamics models is the angle that the propagating detonation wave makes with the charge edge. This is commonly referred to as the boundary angle, and is a property of the explosive/confiner material combination. Such angles can be determined: (i) experimentally from measured detonation wave-shapes, (ii) theoretically, or (iii) via hydrocode simulations using a reactive burn model. Of these approaches: (i) is difficult because of resolution, (ii) breaks down for certain configurations, while (iii) requires a well validated model. In this paper, the CREST reactive burn model, which has previously been successful in modelling a wide range of explosive phenomena, is used to simulate recent Detonation Confinement Sandwich Tests conducted at LANL using the insensitive high explosive PBX 9502. Simulated detonation wave-shapes in PBX 9502 for a number of different confiner materials and combinations closely match those recorded from the experiments. Boundary angles were subsequently extracted from the simulated results via a wave-shape analysis toolkit. The results shown demonstrate the usefulness of CREST in determining detonation wave boundary angles for a range of explosive/confiner material combinations.

Simulating physiological interactions in a hybrid system of mathematical models.

PubMed

Kretschmer, Jörn; Haunsberger, Thomas; Drost, Erick; Koch, Edmund; Möller, Knut

2014-12-01

Mathematical models can be deployed to simulate physiological processes of the human organism. Exploiting these simulations, reactions of a patient to changes in the therapy regime can be predicted. Based on these predictions, medical decision support systems (MDSS) can help in optimizing medical therapy. An MDSS designed to support mechanical ventilation in critically ill patients should not only consider respiratory mechanics but should also consider other systems of the human organism such as gas exchange or blood circulation. A specially designed framework allows combining three model families (respiratory mechanics, cardiovascular dynamics and gas exchange) to predict the outcome of a therapy setting. Elements of the three model families are dynamically combined to form a complex model system with interacting submodels. Tests revealed that complex model combinations are not computationally feasible. In most patients, cardiovascular physiology could be simulated by simplified models decreasing computational costs. Thus, a simplified cardiovascular model that is able to reproduce basic physiological behavior is introduced. This model purely consists of difference equations and does not require special algorithms to be solved numerically. The model is based on a beat-to-beat model which has been extended to react to intrathoracic pressure levels that are present during mechanical ventilation. The introduced reaction to intrathoracic pressure levels as found during mechanical ventilation has been tuned to mimic the behavior of a complex 19-compartment model. Tests revealed that the model is able to represent general system behavior comparable to the 19-compartment model closely. Blood pressures were calculated with a maximum deviation of 1.8 % in systolic pressure and 3.5 % in diastolic pressure, leading to a simulation error of 0.3 % in cardiac output. The gas exchange submodel being reactive to changes in cardiac output showed a resulting deviation of less than 0.1 %. Therefore, the proposed model is usable in combinations where cardiovascular simulation does not have to be detailed. Computing costs have been decreased dramatically by a factor 186 compared to a model combination employing the 19-compartment model.

Effects of Transient Power Extraction on an Integrated Hardware-in-the-Loop Aircraft/Propulsion/Power System

DTIC Science & Technology

2008-11-01

Simulations of an engine and its Full Authority Digital Engine Control ( FADEC ), along with a 6 degree-of-freedom (6DoF) airframe dynamics model and...as needed. In its current configuration, the generic turbine engine model’s FADEC is included in the same simulation and runs primarily on 2 a...back to the engine. As mentioned previously, the FADEC and engine are combined into one simulation and are collectively referred to as “the engine

Prediction of time-integrated activity coefficients in PRRT using simulated dynamic PET and a pharmacokinetic model.

PubMed

Hardiansyah, Deni; Attarwala, Ali Asgar; Kletting, Peter; Mottaghy, Felix M; Glatting, Gerhard

2017-10-01

To investigate the accuracy of predicted time-integrated activity coefficients (TIACs) in peptide-receptor radionuclide therapy (PRRT) using simulated dynamic PET data and a physiologically based pharmacokinetic (PBPK) model. PBPK parameters were estimated using biokinetic data of 15 patients after injection of (152±15)MBq of 111 In-DTPAOC (total peptide amount (5.78±0.25)nmol). True mathematical phantoms of patients (MPPs) were the PBPK model with the estimated parameters. Dynamic PET measurements were simulated as being done after bolus injection of 150MBq 68 Ga-DOTATATE using the true MPPs. Dynamic PET scans around 35min p.i. (P 1 ), 4h p.i. (P 2 ) and the combination of P 1 and P 2 (P 3 ) were simulated. Each measurement was simulated with four frames of 5min each and 2 bed positions. PBPK parameters were fitted to the PET data to derive the PET-predicted MPPs. Therapy was simulated assuming an infusion of 5.1GBq of 90 Y-DOTATATE over 30min in both true and PET-predicted MPPs. TIACs of simulated therapy were calculated, true MPPs (true TIACs) and predicted MPPs (predicted TIACs) followed by the calculation of variabilities v. For P 1 and P 2 the population variabilities of kidneys, liver and spleen were acceptable (v<10%). For the tumours and the remainders, the values were large (up to 25%). For P 3 , population variabilities for all organs including the remainder further improved, except that of the tumour (v>10%). Treatment planning of PRRT based on dynamic PET data seems possible for the kidneys, liver and spleen using a PBPK model and patient specific information. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Evaluation of subgrid-scale models in large-eddy simulations of turbulent flow in a centrifugal pump impeller

NASA Astrophysics Data System (ADS)

Yang, Zhengjun; Wang, Fujun; Zhou, Peijian

2012-09-01

The current research of large eddy simulation (LES) of turbulent flow in pumps mainly concentrates in applying conventional subgrid-scale (SGS) model to simulate turbulent flow, which aims at obtaining the flow field in pump. The selection of SGS model is usually not considered seriously, so the accuracy and efficiency of the simulation cannot be ensured. Three SGS models including Smagorinsky-Lilly model, dynamic Smagorinsky model and dynamic mixed model are comparably studied by using the commercial CFD code Fluent combined with its user define function. The simulations are performed for the turbulent flow in a centrifugal pump impeller. The simulation results indicate that the mean flows predicted by the three SGS models agree well with the experimental data obtained from the test that detailed measurements of the flow inside the rotating passages of a six-bladed shrouded centrifugal pump impeller performed using particle image velocimetry (PIV) and laser Doppler velocimetry (LDV). The comparable results show that dynamic mixed model gives the most accurate results for mean flow in the centrifugal pump impeller. The SGS stress of dynamic mixed model is decompose into the scale similar part and the eddy viscous part. The scale similar part of SGS stress plays a significant role in high curvature regions, such as the leading edge and training edge of pump blade. It is also found that the dynamic mixed model is more adaptive to compute turbulence in the pump impeller. The research results presented is useful to improve the computational accuracy and efficiency of LES for centrifugal pumps, and provide important reference for carrying out simulation in similar fluid machineries.

Experimentally simulating the dynamics of quantum light and matter at ultrastrong coupling using circuit QED (1) - implementation and matter dynamics -

NASA Astrophysics Data System (ADS)

Kounalakis, M.; Langford, N. K.; Sagastizabal, R.; Dickel, C.; Bruno, A.; Luthi, F.; Thoen, D. J.; Endo, A.; Dicarlo, L.

The field dipole coupling of quantum light and matter, described by the quantum Rabi model, leads to exotic phenomena when the coupling strength g becomes comparable or larger than the atom and photon frequencies ωq , r. In this ultra-strong coupling regime, excitations are not conserved, leading to collapse-revival dynamics in atom and photon parity and Schrödinger-cat-like atom-photon entanglement. We realize a quantum simulation of the Rabi model using a transmon qubit coupled to a resonator. In this first part, we describe our analog-digital approach to implement up to 90 symmetric Trotter steps, combining single-qubit gates with the Jaynes-Cummings interaction naturally present in our circuit QED system. Controlling the phase of microwave pulses defines a rotating frame and enables simulation of arbitrary parameter regimes of the Rabi model. We demonstrate measurements of qubit parity dynamics showing revivals at g /ωr > 0 . 8 for ωq = 0 and characteristic dynamics for nondegenerate ωq from g / 4 to g. Funding from the EU FP7 Project ScaleQIT, an ERC Grant, the Dutch Research Organization NWO, and Microsoft Research.

Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations.

PubMed

Hu, Guodong; Xu, Shicai; Wang, Jihua

2015-12-01

Inhibition of p53-MDM2 interaction by small molecules is considered to be a promising approach to re-activate wild-type p53 for tumor suppression. Several inhibitors of the MDM2-p53 interaction were designed and studied by the experimental methods and the molecular dynamics simulation. However, the unbinding mechanism was still unclear. The steered molecular dynamics simulations combined with Brownian dynamics fluctuation-dissipation theorem were employed to obtain the free-energy landscape of unbinding between MDM2 and their four ligands. It was shown that compounds 4 and 8 dissociate faster than compounds 5 and 7. The absolute binding free energies for these four ligands are in close agreement with experimental results. The open movement of helix II and helix IV in the MDM2 protein-binding pocket upon unbinding is also consistent with experimental MDM2-unbound conformation. We further found that different binding mechanisms among different ligands are associated with H-bond with Lys51 and Glu25. These mechanistic results may be useful for improving ligand design. © 2015 John Wiley & Sons A/S.

Rotational and translational dynamics and their relation to hydrogen bond lifetimes in an ionic liquid by means of NMR relaxation time experiments and molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Strate, Anne; Neumann, Jan; Overbeck, Viviane; Bonsa, Anne-Marie; Michalik, Dirk; Paschek, Dietmar; Ludwig, Ralf

2018-05-01

We report a concerted theoretical and experimental effort to determine the reorientational dynamics as well as hydrogen bond lifetimes for the doubly ionic hydrogen bond +OH⋯O- in the ionic liquid (2-hydroxyethyl)trimethylammonium bis(trifluoromethylsulfonyl)imide [Ch][NTf2] by using a combination of NMR relaxation time experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Due to fast proton exchange, the determination of rotational correlation times is challenging. For molecular liquids, 17O-enhanced proton relaxation time experiments have been used to determine the rotational correlation times for the OH vectors in water or alcohols. As an alternative to those expensive isotopic substitution experiments, we employed a recently introduced approach which is providing access to the rotational dynamics from a single NMR deuteron quadrupolar relaxation time experiment. Here, the deuteron quadrupole coupling constants (DQCCs) are obtained from a relation between the DQCC and the δ1H proton chemical shifts determined from a set of DFT calculated clusters in combination with experimentally determined proton chemical shifts. The NMR-obtained rotational correlation times were compared to those obtained from MD simulations and then related to viscosities for testing the applicability of popular hydrodynamic models. In addition, hydrogen bond lifetimes were derived, using hydrogen bond population correlation functions computed from MD simulations. Here, two different time domains were observed: The short-time contributions to the hydrogen lifetimes and the reorientational correlation times have roughly the same size and are located in the picosecond range, whereas the long-time contributions decay with relaxation times in the nanosecond regime and are related to rather slow diffusion processes. The computed average hydrogen bond lifetime is dominated by the long-time process, highlighting the importance and longevity of hydrogen-bonded ion pairs in these ionic liquids.

It's all in the timing: modeling isovolumic contraction through development and disease with a dynamic dual electromechanical bioreactor system.

PubMed

Morgan, Kathy Ye; Black, Lauren Deems

2014-01-01

This commentary discusses the rationale behind our recently reported work entitled "Mimicking isovolumic contraction with combined electromechanical stimulation improves the development of engineered cardiac constructs," introduces new data supporting our hypothesis, and discusses future applications of our bioreactor system. The ability to stimulate engineered cardiac tissue in a bioreactor system that combines both electrical and mechanical stimulation offers a unique opportunity to simulate the appropriate dynamics between stretch and contraction and model isovolumic contraction in vitro. Our previous study demonstrated that combined electromechanical stimulation that simulated the timing of isovolumic contraction in healthy tissue improved force generation via increased contractile and calcium handling protein expression and improved hypertrophic pathway activation. In new data presented here, we further demonstrate that modification of the timing between electrical and mechanical stimulation to mimic a non-physiological process negatively impacts the functionality of the engineered constructs. We close by exploring the various disease states that have altered timing between the electrical and mechanical stimulation signals as potential future directions for the use of this system.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.

PubMed

Wall, Michael E

2018-03-01

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wall, Michael E.

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.

2018-01-25

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation

NASA Astrophysics Data System (ADS)

Saez, David Adrian; Vöhringer-Martinez, Esteban

2015-10-01

S-Adenosylmethionine (AdoMet) is involved in many biological processes as cofactor in enzymes transferring its sulfonium methyl group to various substrates. Additionally, it is used as drug and nutritional supplement to reduce the pain in osteoarthritis and against depression. Due to the biological relevance of AdoMet it has been part of various computational simulation studies and will also be in the future. However, to our knowledge no rigorous force field parameter development for its simulation in biological systems has been reported. Here, we use electronic structure calculations combined with molecular dynamics simulations in explicit solvent to develop force field parameters compatible with the AMBER99 force field. Additionally, we propose new dynamic Hirshfeld-I atomic charges which are derived from the polarized electron density of AdoMet in aqueous solution to describe its electrostatic interactions in biological systems. The validation of the force field parameters and the atomic charges is performed against experimental interproton NOE distances of AdoMet in aqueous solution and crystal structures of AdoMet in the cavity of three representative proteins.

Neutron powder diffraction and molecular simulation study of the structural evolution of ammonia borane from 15 to 340 K.

PubMed

Hess, Nancy J; Schenter, Gregory K; Hartman, Michael R; Daemen, Luc L; Proffen, Thomas; Kathmann, Shawn M; Mundy, Christopher J; Hartl, Monika; Heldebrant, David J; Stowe, Ashley C; Autrey, Tom

2009-05-14

The structural behavior of (11)B-, (2)H-enriched ammonia borane, ND(3)(11)BD(3), over the temperature range from 15 to 340 K was investigated using a combination of neutron powder diffraction and ab initio molecular dynamics simulations. In the low temperature orthorhombic phase, the progressive displacement of the borane group under the amine group was observed leading to the alignment of the B-N bond near parallel to the c-axis. The orthorhombic to tetragonal structural phase transition at 225 K is marked by dramatic change in the dynamics of both the amine and borane group. The resulting hydrogen disorder is problematic to extract from the metrics provided by Rietveld refinement but is readily apparent in molecular dynamics simulation and in difference Fourier transform maps. At the phase transition, Rietveld refinement does indicate a disruption of one of two dihydrogen bonds that link adjacent ammonia borane molecules. Metrics determined by Rietveld refinement are in excellent agreement with those determined from molecular simulation. This study highlights the valuable insights added by coupled experimental and computational studies.

Influence of model order reduction methods on dynamical-optical simulations

NASA Astrophysics Data System (ADS)

Störkle, Johannes; Eberhard, Peter

2017-04-01

In this work, the influence of model order reduction (MOR) methods on optical aberrations is analyzed within a dynamical-optical simulation of a high precision optomechanical system. Therefore, an integrated modeling process and new methods have to be introduced for the computation and investigation of the overall dynamical-optical behavior. For instance, this optical system can be a telescope optic or a lithographic objective. In order to derive a simplified mechanical model for transient time simulations with low computational cost, the method of elastic multibody systems in combination with MOR methods can be used. For this, software tools and interfaces are defined and created. Furthermore, mechanical and optical simulation models are derived and implemented. With these, on the one hand, the mechanical sensitivity can be investigated for arbitrary external excitations and on the other hand, the related optical behavior can be predicted. In order to clarify these methods, academic examples are chosen and the influences of the MOR methods and simulation strategies are analyzed. Finally, the systems are investigated with respect to the mechanical-optical frequency responses, and in conclusion, some recommendations for the application of reduction methods are given.

Mechanism of Acetylcholinesterase Inhibition by Fasciculin: A 5-ns Molecular Dynamics Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tai, Kaihsu; Shen, T Y.; Henchman, Richard H.

Our previous molecular dynamics simulation (10 ns) of mouse acetylcholinesterase (EC 3.1.1.7) revealed complex fluctuation of the enzyme active site gorge. Now we report a 5-ns simulation of acetylcholinesterase complexed with fasciculin 2. Fasciculin 2 binds to the gorge entrance of acetylcholinesterase with excellent complementarity and many polar and hydrophobic interactions. In this simulation of the protein-protein complex, where fasciculin 2 appears to sterically block access of ligands to the gorge, again we observe a two-peaked probability distribution of the gorge width. When fasciculin is present, the gorge width distribution is altered such that the gorge is more likely tomore » be narrow. Moreover, there are large increases in the opening of alternative passages, namely, the side door (near Thr 75) and the back door (near Tyr 449). Finally, the catalytic triad arrangement in the acetylcholinesterase active site is disrupted with fasciculin bound. These data support that, in addition to the steric obstruction seen in the crystal structure, fasciculin may inhibit acetylcholinesterase by combined allosteric and dynamical means. Additional data from these simulations can be found at http://mccammon.ucsd.edu/.« less

Effects of simulator motion and visual characteristics on rotorcraft handling qualities evaluations

NASA Technical Reports Server (NTRS)

Mitchell, David G.; Hart, Daniel C.

1993-01-01

The pilot's perceptions of aircraft handling qualities are influenced by a combination of the aircraft dynamics, the task, and the environment under which the evaluation is performed. When the evaluation is performed in a groundbased simulator, the characteristics of the simulation facility also come into play. Two studies were conducted on NASA Ames Research Center's Vertical Motion Simulator to determine the effects of simulator characteristics on perceived handling qualities. Most evaluations were conducted with a baseline set of rotorcraft dynamics, using a simple transfer-function model of an uncoupled helicopter, under different conditions of visual time delays and motion command washout filters. Differences in pilot opinion were found as the visual and motion parameters were changed, reflecting a change in the pilots' perceptions of handling qualities, rather than changes in the aircraft model itself. The results indicate a need for tailoring the motion washout dynamics to suit the task. Visual-delay data are inconclusive but suggest that it may be better to allow some time delay in the visual path to minimize the mismatch between visual and motion, rather than eliminate the visual delay entirely through lead compensation.

Protein dynamics in organic media at varying water activity studied by molecular dynamics simulation.

PubMed

Wedberg, Rasmus; Abildskov, Jens; Peters, Günther H

2012-03-01

In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method relies on determining the water content of the bulk phase and uses a combination of Kirkwood-Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme structure and flexibility.

Single-Molecule Probing the Energy Landscape of Enzymatic Reaction and Non-Covalent Interactions

NASA Astrophysics Data System (ADS)

Lu, H. Peter; Hu, Dehong; Chen, Yu; Vorpagel, Erich R.

2002-03-01

We have applied single-molecule spectroscopy under physiological conditions to study the mechanisms and dynamics of T4 lysozyme enzymatic reactions, characterizing mode-specific protein conformational dynamics. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time. The overall reaction rates were found to vary widely from molecule-to-molecule, and the initial non-specific binding of the enzyme to the substrate was seen to dominate this inhomogeneity. The reaction steps subsequent to the initial binding were found to have homogeneous rates. Molecular dynamics simulation has been applied to elucidate the mechanism and intermediate states of the single-molecule enzymatic reaction. Combining the analysis of single-molecule experimental trajectories, MD simulation trajectories, and statistical modeling, we have revealed the nature of multiple intermediate states involved in the active enzyme-substrate complex formation and the associated conformational change mechanism and dynamics.

Simulation of magnetic active polymers for versatile microfluidic devices

NASA Astrophysics Data System (ADS)

Gusenbauer, Markus; Özelt, Harald; Fischbacher, Johann; Reichel, Franz; Exl, Lukas; Bance, Simon; Kataeva, Nadezhda; Binder, Claudia; Brückl, Hubert; Schrefl, Thomas

2013-01-01

We propose to use a compound of magnetic nanoparticles (20-100 nm) embedded in a flexible polymer (Polydimethylsiloxane PDMS) to filter circulating tumor cells (CTCs). The analysis of CTCs is an emerging tool for cancer biology research and clinical cancer management including the detection, diagnosis and monitoring of cancer. The combination of experiments and simulations lead to a versatile microfluidic lab-on-chip device. Simulations are essential to understand the influence of the embedded nanoparticles in the elastic PDMS when applying a magnetic gradient field. It combines finite element calculations of the polymer, magnetic simulations of the embedded nanoparticles and the fluid dynamic calculations of blood plasma and blood cells. With the use of magnetic active polymers a wide range of tunable microfluidic structures can be created. The method can help to increase the yield of needed isolated CTCs.

Composite Load Spectra for Select Space Propulsion Structural Components

NASA Technical Reports Server (NTRS)

Ho, Hing W.; Newell, James F.

1994-01-01

Generic load models are described with multiple levels of progressive sophistication to simulate the composite (combined) load spectra (CLS) that are induced in space propulsion system components, representative of Space Shuttle Main Engines (SSME), such as transfer ducts, turbine blades and liquid oxygen (LOX) posts. These generic (coupled) models combine the deterministic models for composite load dynamic, acoustic, high-pressure and high rotational speed, etc., load simulation using statistically varying coefficients. These coefficients are then determined using advanced probabilistic simulation methods with and without strategically selected experimental data. The entire simulation process is included in a CLS computer code. Applications of the computer code to various components in conjunction with the PSAM (Probabilistic Structural Analysis Method) to perform probabilistic load evaluation and life prediction evaluations are also described to illustrate the effectiveness of the coupled model approach.

Graph-based linear scaling electronic structure theory.

PubMed

Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Graph-based linear scaling electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Nonlinear Model Predictive Control with Constraint Satisfactions for a Quadcopter

NASA Astrophysics Data System (ADS)

Wang, Ye; Ramirez-Jaime, Andres; Xu, Feng; Puig, Vicenç

2017-01-01

This paper presents a nonlinear model predictive control (NMPC) strategy combined with constraint satisfactions for a quadcopter. The full dynamics of the quadcopter describing the attitude and position are nonlinear, which are quite sensitive to changes of inputs and disturbances. By means of constraint satisfactions, partial nonlinearities and modeling errors of the control-oriented model of full dynamics can be transformed into the inequality constraints. Subsequently, the quadcopter can be controlled by an NMPC controller with the updated constraints generated by constraint satisfactions. Finally, the simulation results applied to a quadcopter simulator are provided to show the effectiveness of the proposed strategy.

A combined molecular dynamics/micromechanics/finite element approach for multiscale constitutive modeling of nanocomposites with interface effects

NASA Astrophysics Data System (ADS)

Yang, B. J.; Shin, H.; Lee, H. K.; Kim, H.

2013-12-01

We introduce a multiscale framework based on molecular dynamic (MD) simulation, micromechanics, and finite element method (FEM). A micromechanical model, which considers influences of the interface properties, nanoparticle (NP) size, and microcracks, is developed. Then, we perform MD simulations to characterize the mechanical properties of the nanocomposite system (silica/nylon 6) with varying volume fraction and size of NPs. By comparing the MD with micromechanics results, intrinsic physical properties at interfacial region are derived. Finally, we implement the developed model in the FEM code with the derived interfacial parameters, and predict the mechanical behavior of the nanocomposite at the macroscopic scale.

Study of Dynamic Characteristics of Aeroelastic Systems Utilizing Randomdec Signatures

NASA Technical Reports Server (NTRS)

Chang, C. S.

1975-01-01

The feasibility of utilizing the random decrement method in conjunction with a signature analysis procedure to determine the dynamic characteristics of an aeroelastic system for the purpose of on-line prediction of potential on-set of flutter was examined. Digital computer programs were developed to simulate sampled response signals of a two-mode aeroelastic system. Simulated response data were used to test the random decrement method. A special curve-fit approach was developed for analyzing the resulting signatures. A number of numerical 'experiments' were conducted on the combined processes. The method is capable of determining frequency and damping values accurately from randomdec signatures of carefully selected lengths.

A resilient and efficient CFD framework: Statistical learning tools for multi-fidelity and heterogeneous information fusion

NASA Astrophysics Data System (ADS)

Lee, Seungjoon; Kevrekidis, Ioannis G.; Karniadakis, George Em

2017-09-01

Exascale-level simulations require fault-resilient algorithms that are robust against repeated and expected software and/or hardware failures during computations, which may render the simulation results unsatisfactory. If each processor can share some global information about the simulation from a coarse, limited accuracy but relatively costless auxiliary simulator we can effectively fill-in the missing spatial data at the required times by a statistical learning technique - multi-level Gaussian process regression, on the fly; this has been demonstrated in previous work [1]. Based on the previous work, we also employ another (nonlinear) statistical learning technique, Diffusion Maps, that detects computational redundancy in time and hence accelerate the simulation by projective time integration, giving the overall computation a "patch dynamics" flavor. Furthermore, we are now able to perform information fusion with multi-fidelity and heterogeneous data (including stochastic data). Finally, we set the foundations of a new framework in CFD, called patch simulation, that combines information fusion techniques from, in principle, multiple fidelity and resolution simulations (and even experiments) with a new adaptive timestep refinement technique. We present two benchmark problems (the heat equation and the Navier-Stokes equations) to demonstrate the new capability that statistical learning tools can bring to traditional scientific computing algorithms. For each problem, we rely on heterogeneous and multi-fidelity data, either from a coarse simulation of the same equation or from a stochastic, particle-based, more "microscopic" simulation. We consider, as such "auxiliary" models, a Monte Carlo random walk for the heat equation and a dissipative particle dynamics (DPD) model for the Navier-Stokes equations. More broadly, in this paper we demonstrate the symbiotic and synergistic combination of statistical learning, domain decomposition, and scientific computing in exascale simulations.

Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory.

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2017-11-15

A self-consistent scheme combining the molecular dynamics (MD) simulation and density functional theory (DFT) was recently proposed to incorporate the effects of the charge transfer and polarization of ions into non-poralizable force fields of ionic liquids for improved description of energetics and dynamics. The purpose of the present work is to analyze the detailed setups of the MD/DFT scheme by focusing on how the basis set, exchange-correlation (XC) functional, charge-fitting method or force field for the intramolecular and Lennard-Jones interactions affects the MD/DFT results of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ( [C1mim][NTf2]) and 1-ethyl-3-methylimidazolium glycinate ( [C2mim][Gly]). It was found that the double-zeta valence polarized or larger size of basis set is required for the convergence of the effective charge of the ion. The choice of the XC functional was further not influential as far as the generalized gradient approximation is used. The charge-fitting method and force field govern the accuracy of the MD/DFT scheme, on the other hand. We examined the charge-fitting methods of Blöchl, the iterative Hirshfeld (Hirshfeld-I), and REPEAT in combination with Lopes et al.'s force field and general AMBER force field. There is no single combination of charge fitting and force field that provides good agreements with the experiments, while the MD/DFT scheme reduces the effective charges of the ions and leads to better description of energetics and dynamics compared to the original force field with unit charges. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

PubMed Central

Carvalho, Alexandra T P; Gouveia, Leonor; Kanna, Charan Raju; Wärmländer, Sebastian K T S; Platts, Jamie A; Kamerlin, Shina Caroline Lynn

2014-01-01

We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding. PMID:25625845

Aeroelastic modeling for the FIT team F/A-18 simulation

NASA Technical Reports Server (NTRS)

Zeiler, Thomas A.; Wieseman, Carol D.

1989-01-01

Some details of the aeroelastic modeling of the F/A-18 aircraft done for the Functional Integration Technology (FIT) team's research in integrated dynamics modeling and how these are combined with the FIT team's integrated dynamics model are described. Also described are mean axis corrections to elastic modes, the addition of nonlinear inertial coupling terms into the equations of motion, and the calculation of internal loads time histories using the integrated dynamics model in a batch simulation program. A video tape made of a loads time history animation was included as a part of the oral presentation. Also discussed is work done in one of the areas of unsteady aerodynamic modeling identified as needing improvement, specifically, in correction factor methodologies for improving the accuracy of stability derivatives calculated with a doublet lattice code.

Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

PubMed Central

Wen, Bin; Peng, Junhui; Zuo, Xiaobing; Gong, Qingguo; Zhang, Zhiyong

2014-01-01

Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations. PMID:25140431

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.

PubMed

Luginbühl, P; Güntert, P; Billeter, M; Wüthrich, K

1996-09-01

A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.

Radionuclide Incorporation and Long Term Performance of Apatite Waste Forms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jianwei; Lian, Jie; Gao, Fei

2016-01-04

This project aims to combines state-of-the-art experimental and characterization techniques with atomistic simulations based on density functional theory (DFT) and molecular dynamics (MD) simulations. With an initial focus on long-lived I-129 and other radionuclides such as Cs, Sr in apatite structure, specific research objectives include the atomic scale understanding of: (1) incorporation behavior of the radionuclides and their effects on the crystal chemistry and phase stability; (2) stability and microstructure evolution of designed waste forms under coupled temperature and radiation environments; (3) incorporation and migration energetics of radionuclides and release behaviors as probed by DFT and molecular dynamics (MD) simulations;more » and (4) chemical durability as measured in dissolution experiments for long term performance evaluation and model validation.« less

Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates.

PubMed

Zhang, Weihong; Howell, Steven C; Wright, David W; Heindel, Andrew; Qiu, Xiangyun; Chen, Jianhan; Curtis, Joseph E

2017-05-01

We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynamics simulations to create ensembles of structures to model a wide variety of soft-matter biological systems. Our particular emphasis is focused on modeling low-resolution small-angle scattering and reflectivity structural data. We provide examples of this method applied to HIV-1 Gag protein and derived fragment proteins, TraI protein, linear B-DNA, a nucleosome core particle, and a glycosylated monoclonal antibody. This procedure will enable a large community of researchers to model low-resolution experimental data with greater accuracy by using robust physics based simulation and sampling methods which are a significant improvement over traditional methods used to interpret such data. Published by Elsevier Inc.

Neural network identification of aircraft nonlinear aerodynamic characteristics

NASA Astrophysics Data System (ADS)

Egorchev, M. V.; Tiumentsev, Yu V.

2018-02-01

The simulation problem for the controlled aircraft motion is considered in the case of imperfect knowledge of the modeling object and its operating conditions. The work aims to develop a class of modular semi-empirical dynamic models that combine the capabilities of theoretical and neural network modeling. We consider the use of semi-empirical neural network models for solving the problem of identifying aerodynamic characteristics of an aircraft. We also discuss the formation problem for a representative set of data characterizing the behavior of a simulated dynamic system, which is one of the critical tasks in the synthesis of ANN-models. The effectiveness of the proposed approach is demonstrated using a simulation example of the aircraft angular motion and identifying the corresponding coefficients of aerodynamic forces and moments.

Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes.

PubMed

Araujo, Gabriela C; Silva, Ricardo H T; Scott, Luis P B; Araujo, Alexandre S; Souza, Fatima P; de Oliveira, Ronaldo Junio

2016-12-01

The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not well known. Studies show that SH protein increases RSV virulence degree and permeability to small compounds, suggesting it is involved in the formation of ion channels. The knowledge of SH structure and function is fundamental for a better understanding of its infection mechanism. The aim of this study was to model, characterize, and analyze the structural behavior of SH protein in the phospholipids bilayer environment. Molecular modeling of SH pentameric structure was performed, followed by traditional molecular dynamics (MD) simulations of the protein immersed in the lipid bilayer. Molecular dynamics with excited normal modes (MDeNM) was applied in the resulting system in order to investigate long time scale pore dynamics. MD simulations support that SH protein is stable in its pentameric form. Simulations also showed the presence of water molecules within the bilayer by density distribution, thus confirming that SH protein is a viroporin. This water transport was also observed in MDeNM studies with histidine residues of five chains (His22 and His51), playing a key role in pore permeability. The combination of traditional MD and MDeNM was a very efficient protocol to investigate functional conformational changes of transmembrane proteins that act as molecular channels. This protocol can support future investigations of drug candidates by acting on SH protein to inhibit viral infection. Graphical Abstract The ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domainᅟ.

Computer Simulations and Theoretical Studies of Complex Systems: from complex fluids to frustrated magnets

NASA Astrophysics Data System (ADS)

Choi, Eunsong

Computer simulations are an integral part of research in modern condensed matter physics; they serve as a direct bridge between theory and experiment by systemactically applying a microscopic model to a collection of particles that effectively imitate a macroscopic system. In this thesis, we study two very differnt condensed systems, namely complex fluids and frustrated magnets, primarily by simulating classical dynamics of each system. In the first part of the thesis, we focus on ionic liquids (ILs) and polymers--the two complementary classes of materials that can be combined to provide various unique properties. The properties of polymers/ILs systems, such as conductivity, viscosity, and miscibility, can be fine tuned by choosing an appropriate combination of cations, anions, and polymers. However, designing a system that meets a specific need requires a concrete understanding of physics and chemistry that dictates a complex interplay between polymers and ionic liquids. In this regard, molecular dynamics (MD) simulation is an efficient tool that provides a molecular level picture of such complex systems. We study the behavior of Poly (ethylene oxide) (PEO) and the imidazolium based ionic liquids, using MD simulations and statistical mechanics. We also discuss our efforts to develop reliable and efficient classical force-fields for PEO and the ionic liquids. The second part is devoted to studies on geometrically frustrated magnets. In particular, a microscopic model, which gives rise to an incommensurate spiral magnetic ordering observed in a pyrochlore antiferromagnet is investigated. The validation of the model is made via a comparison of the spin-wave spectra with the neutron scattering data. Since the standard Holstein-Primakoff method is difficult to employ in such a complex ground state structure with a large unit cell, we carry out classical spin dynamics simulations to compute spin-wave spectra directly from the Fourier transform of spin trajectories. We conclude the study by showing an excellent agreement between the simulation and the experiment.

The Influence of 150-Cavity Binders on the Dynamics of Influenza A Neuraminidases as Revealed by Molecular Dynamics Simulations and Combined Clustering

PubMed Central

Greenway, Kyle T.; LeGresley, Eric B.; Pinto, B. Mario

2013-01-01

Neuraminidase inhibitors are the main pharmaceutical agents employed for treatments of influenza infections. The neuraminidase structures typically exhibit a 150-cavity, an exposed pocket that is adjacent to the catalytic site. This site offers promising additional contact points for improving potency of existing pharmaceuticals, as well as generating entirely new candidate inhibitors. Several inhibitors based on known compounds and designed to interact with 150-cavity residues have been reported. However, the dynamics of any of these inhibitors remains unstudied and their viability remains unknown. This work reports the outcome of long-term, all-atom molecular dynamics simulations of four such inhibitors, along with three standard inhibitors for comparison. Each is studied in complex with four representative neuraminidase structures, which are also simulated in the absence of ligands for comparison, resulting in a total simulation time of 9.6µs. Our results demonstrate that standard inhibitors characteristically reduce the mobility of these dynamic proteins, while the 150-binders do not, instead giving rise to many unique conformations. We further describe an improved RMSD-based clustering technique that isolates these conformations – the structures of which are provided to facilitate future molecular docking studies – and reveals their interdependence. We find that this approach confers many advantages over previously described techniques, and the implications for rational drug design are discussed. PMID:23544106

The influence of 150-cavity binders on the dynamics of influenza A neuraminidases as revealed by molecular dynamics simulations and combined clustering.

PubMed

Greenway, Kyle T; LeGresley, Eric B; Pinto, B Mario

2013-01-01

Neuraminidase inhibitors are the main pharmaceutical agents employed for treatments of influenza infections. The neuraminidase structures typically exhibit a 150-cavity, an exposed pocket that is adjacent to the catalytic site. This site offers promising additional contact points for improving potency of existing pharmaceuticals, as well as generating entirely new candidate inhibitors. Several inhibitors based on known compounds and designed to interact with 150-cavity residues have been reported. However, the dynamics of any of these inhibitors remains unstudied and their viability remains unknown. This work reports the outcome of long-term, all-atom molecular dynamics simulations of four such inhibitors, along with three standard inhibitors for comparison. Each is studied in complex with four representative neuraminidase structures, which are also simulated in the absence of ligands for comparison, resulting in a total simulation time of 9.6 µs. Our results demonstrate that standard inhibitors characteristically reduce the mobility of these dynamic proteins, while the 150-binders do not, instead giving rise to many unique conformations. We further describe an improved RMSD-based clustering technique that isolates these conformations--the structures of which are provided to facilitate future molecular docking studies--and reveals their interdependence. We find that this approach confers many advantages over previously described techniques, and the implications for rational drug design are discussed.

Microscopic modeling of gas-surface scattering. I. A combined molecular dynamics-rate equation approach

NASA Astrophysics Data System (ADS)

Filinov, A.; Bonitz, M.; Loffhagen, D.

2018-06-01

A combination of first principle molecular dynamics (MD) simulations with a rate equation model (MD-RE approach) is presented to study the trapping and the scattering of rare gas atoms from metal surfaces. The temporal evolution of the atom fractions that are either adsorbed or scattered into the continuum is investigated in detail. We demonstrate that for this description one has to consider trapped, quasi-trapped and scattering states, and present an energetic definition of these states. The rate equations contain the transition probabilities between the states. We demonstrate how these rate equations can be derived from kinetic theory. Moreover, we present a rigorous way to determine the transition probabilities from a microscopic analysis of the particle trajectories generated by MD simulations. Once the system reaches quasi-equilibrium, the rates converge to stationary values, and the subsequent thermal adsorption/desorption dynamics is completely described by the rate equations without the need to perform further time-consuming MD simulations. As a proof of concept of our approach, MD simulations for argon atoms interacting with a platinum (111) surface are presented. A detailed deterministic trajectory analysis is performed, and the transition rates are constructed. The dependence of the rates on the incidence conditions and the lattice temperature is analyzed. Based on this example, we analyze the time scale of the gas-surface system to approach the quasi-stationary state. The MD-RE model has great relevance for the plasma-surface modeling as it makes an extension of accurate simulations to long, experimentally relevant time scales possible. Its application to the computation of atomic sticking probabilities is given in the second part (paper II).

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory

NASA Astrophysics Data System (ADS)

Langenbach, K.; Heilig, M.; Horsch, M.; Hasse, H.

2018-03-01

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO2). The molecular model of CO2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory.

PubMed

Langenbach, K; Heilig, M; Horsch, M; Hasse, H

2018-03-28

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO 2 ). The molecular model of CO 2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

Enhanced dynamics of hydrated tRNA on nanodiamond surfaces: A combined neutron scattering and MD simulation study

DOE PAGES

Dhindsa, Gurpreet K.; Bhowmik, Debsindhu; Goswami, Monojoy; ...

2016-09-01

Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on NDmore » surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. As a result, our new findings may provide new design principles for safer, improved drug delivery platforms.« less

Dynamic modeling and motion simulation for a winged hybrid-driven underwater glider

NASA Astrophysics Data System (ADS)

Wang, Shu-Xin; Sun, Xiu-Jun; Wang, Yan-Hui; Wu, Jian-Guo; Wang, Xiao-Ming

2011-03-01

PETREL, a winged hybrid-driven underwater glider is a novel and practical marine survey platform which combines the features of legacy underwater glider and conventional AUV (autonomous underwater vehicle). It can be treated as a multi-rigid-body system with a floating base and a particular hydrodynamic profile. In this paper, theorems on linear and angular momentum are used to establish the dynamic equations of motion of each rigid body and the effect of translational and rotational motion of internal masses on the attitude control are taken into consideration. In addition, due to the unique external shape with fixed wings and deflectable rudders and the dual-drive operation in thrust and glide modes, the approaches of building dynamic model of conventional AUV and hydrodynamic model of submarine are introduced, and the tailored dynamic equations of the hybrid glider are formulated. Moreover, the behaviors of motion in glide and thrust operation are analyzed based on the simulation and the feasibility of the dynamic model is validated by data from lake field trials.

Explicit symplectic algorithms based on generating functions for charged particle dynamics.

PubMed

Zhang, Ruili; Qin, Hong; Tang, Yifa; Liu, Jian; He, Yang; Xiao, Jianyuan

2016-07-01

Dynamics of a charged particle in the canonical coordinates is a Hamiltonian system, and the well-known symplectic algorithm has been regarded as the de facto method for numerical integration of Hamiltonian systems due to its long-term accuracy and fidelity. For long-term simulations with high efficiency, explicit symplectic algorithms are desirable. However, it is generally believed that explicit symplectic algorithms are only available for sum-separable Hamiltonians, and this restriction limits the application of explicit symplectic algorithms to charged particle dynamics. To overcome this difficulty, we combine the familiar sum-split method and a generating function method to construct second- and third-order explicit symplectic algorithms for dynamics of charged particle. The generating function method is designed to generate explicit symplectic algorithms for product-separable Hamiltonian with form of H(x,p)=p_{i}f(x) or H(x,p)=x_{i}g(p). Applied to the simulations of charged particle dynamics, the explicit symplectic algorithms based on generating functions demonstrate superiorities in conservation and efficiency.

Explicit symplectic algorithms based on generating functions for charged particle dynamics

NASA Astrophysics Data System (ADS)

Zhang, Ruili; Qin, Hong; Tang, Yifa; Liu, Jian; He, Yang; Xiao, Jianyuan

2016-07-01

Dynamics of a charged particle in the canonical coordinates is a Hamiltonian system, and the well-known symplectic algorithm has been regarded as the de facto method for numerical integration of Hamiltonian systems due to its long-term accuracy and fidelity. For long-term simulations with high efficiency, explicit symplectic algorithms are desirable. However, it is generally believed that explicit symplectic algorithms are only available for sum-separable Hamiltonians, and this restriction limits the application of explicit symplectic algorithms to charged particle dynamics. To overcome this difficulty, we combine the familiar sum-split method and a generating function method to construct second- and third-order explicit symplectic algorithms for dynamics of charged particle. The generating function method is designed to generate explicit symplectic algorithms for product-separable Hamiltonian with form of H (x ,p ) =pif (x ) or H (x ,p ) =xig (p ) . Applied to the simulations of charged particle dynamics, the explicit symplectic algorithms based on generating functions demonstrate superiorities in conservation and efficiency.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.

PubMed

Shao, Qiang; Shi, Jiye; Zhu, Weiliang

2012-09-28

The ability of molecular dynamics simulation to capturing the transient states within the folding pathway of protein is important to the understanding of protein folding mechanism. In the present study, the integrated-tempering-sampling molecular dynamics (ITS-MD) simulation was performed to investigate the transient states including intermediate and unfolded ones in the folding pathway of a miniprotein, Trp-cage. Three force fields (FF03, FF99SB, and FF96) were tested, and both intermediate and unfolded states with their characteristics in good agreement with experiments were observed during the simulations, which supports the hypothesis that observable intermediates might present in the folding pathway of small polypeptides. In addition, it was demonstrated that FF03 force field as combined with ITS-MD is in overall a more proper force field than the others in reproducing experimentally recorded properties in UVRS, ECD, and NMR, Photo-CIDNP NMR, and IR T-jump experiments, and the folding∕unfolding thermodynamics parameters, such as ΔG(U), ΔC(p), and ΔH(U) (T(m)). In summary, the present study showed that using suitable force field and energy sampling method, molecular dynamics simulation could capture the transient states within the folding pathway of protein which are consistent with the experimental measurements, and thus provide information of protein folding mechanism and thermodynamics.

Effects of Aircraft Wake Dynamics on Measured and Simulated NO(x) and HO(x) Wake Chemistry. Appendix B

NASA Technical Reports Server (NTRS)

Lewellen, D. C.; Lewellen, W. S.

2001-01-01

High-resolution numerical large-eddy simulations of the near wake of a B757 including simplified NOx and HOx chemistry were performed to explore the effects of dynamics on chemistry in wakes of ages from a few seconds to several minutes. Dilution plays an important basic role in the NOx-O3 chemistry in the wake, while a more interesting interaction between the chemistry and dynamics occurs for the HOx species. These simulation results are compared with published measurements of OH and HO2 within a B757 wake under cruise conditions in the upper troposphere taken during the Subsonic Aircraft Contrail and Cloud Effects Special Study (SUCCESS) mission in May 1996. The simulation provides a much finer grained representation of the chemistry and dynamics of the early wake than is possible from the 1 s data samples taken in situ. The comparison suggests that the previously reported discrepancy of up to a factor of 20 - 50 between the SUCCESS measurements of the [HO2]/[OH] ratio and that predicted by simplified theoretical computations is due to the combined effects of large mixing rates around the wake plume edges and averaging over volumes containing large species fluctuations. The results demonstrate the feasibility of using three-dimensional unsteady large-eddy simulations with coupled chemistry to study such phenomena.

Fault Gauge Numerical Simulation : Dynamic Rupture Propagation and Local Energy Partitioning

NASA Astrophysics Data System (ADS)

Mollon, G.

2017-12-01

In this communication, we present dynamic simulations of the local (centimetric) behaviour of a fault filled with a granular gauge submitted to dynamic rupture. The numerical tool (Fig. 1) combines classical Discrete Element Modelling (albeit with the ability to deal with arbitrary grain shapes) for the simualtion of the gauge, and continuous modelling for the simulation of the acoustic waves emission and propagation. In a first part, the model is applied to the simulation of steady-state shearing of the fault under remote displacement boudary conditions, in order to observe the shear accomodation at the interface (R1 cracks, localization, wear, etc.). It also makes it possible to fit to desired values the Rate and State Friction properties of the granular gauge by adapting the contact laws between grains. Such simulations provide quantitative insight in the steady-state energy partitionning between fracture, friction and acoustic emissions as a function of the shear rate. In a second part, the model is submitted to dynamic rupture. For that purpose, the fault is elastically preloaded just below rupture, and a displacement pulse is applied at one end of the sample (and on only one side of the fault). This allows to observe the propagation of the instability along the fault and the interplay between this propagation and the local granular phenomena. Energy partitionning is then observed both in space and time.

Particle-based simulations of self-motile suspensions

NASA Astrophysics Data System (ADS)

Hinz, Denis F.; Panchenko, Alexander; Kim, Tae-Yeon; Fried, Eliot

2015-11-01

A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source software package LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent concentration, pairwise dissipative interactions, and Stokes friction on the statistics of the system are provided. The simulations are used to explore the influence of hydrodynamic interactions in active suspensions. For high agent concentrations in combination with dominating pairwise dissipative forces, strongly correlated motion patterns and a fluid-like spectral distributions of kinetic energy are found. In contrast, systems dominated by Stokes friction exhibit weaker spatial correlations of the velocity field. These results indicate that hydrodynamic interactions may play an important role in the formation of spatially extended structures in active suspensions.

Passive-dynamic ankle-foot orthosis replicates soleus but not gastrocnemius muscle function during stance in gait: Insights for orthosis prescription.

PubMed

Arch, Elisa S; Stanhope, Steven J; Higginson, Jill S

2016-10-01

Passive-dynamic ankle-foot orthosis characteristics, including bending stiffness, should be customized for individuals. However, while conventions for customizing passive-dynamic ankle-foot orthosis characteristics are often described and implemented in clinical practice, there is little evidence to explain their biomechanical rationale. To develop and combine a model of a customized passive-dynamic ankle-foot orthosis with a healthy musculoskeletal model and use simulation tools to explore the influence of passive-dynamic ankle-foot orthosis bending stiffness on plantar flexor function during gait. Dual case study. The customized passive-dynamic ankle-foot orthosis characteristics were integrated into a healthy musculoskeletal model available in OpenSim. Quasi-static forward dynamic simulations tracked experimental gait data under several passive-dynamic ankle-foot orthosis conditions. Predicted muscle activations were calculated through a computed muscle control optimization scheme. Simulations predicted that the passive-dynamic ankle-foot orthoses substituted for soleus but not gastrocnemius function. Induced acceleration analyses revealed the passive-dynamic ankle-foot orthosis acts like a uniarticular plantar flexor by inducing knee extension accelerations, which are counterproductive to natural knee kinematics in early midstance. These passive-dynamic ankle-foot orthoses can provide plantar flexion moments during mid and late stance to supplement insufficient plantar flexor strength. However, the passive-dynamic ankle-foot orthoses negatively influenced knee kinematics in early midstance. Identifying the role of passive-dynamic ankle-foot orthosis stiffness during gait provides biomechanical rationale for how to customize passive-dynamic ankle-foot orthoses for patients. Furthermore, these findings can be used in the future as the basis for developing objective prescription models to help drive the customization of passive-dynamic ankle-foot orthosis characteristics. © The International Society for Prosthetics and Orthotics 2015.

Dispersive models describing mosquitoes’ population dynamics

NASA Astrophysics Data System (ADS)

Yamashita, W. M. S.; Takahashi, L. T.; Chapiro, G.

2016-08-01

The global incidences of dengue and, more recently, zica virus have increased the interest in studying and understanding the mosquito population dynamics. Understanding this dynamics is important for public health in countries where climatic and environmental conditions are favorable for the propagation of these diseases. This work is based on the study of nonlinear mathematical models dealing with the life cycle of the dengue mosquito using partial differential equations. We investigate the existence of traveling wave solutions using semi-analytical method combining dynamical systems techniques and numerical integration. Obtained solutions are validated through numerical simulations using finite difference schemes.

A new approach for modular robot system behavioral modeling: Base on Petri net and category theory

NASA Astrophysics Data System (ADS)

Zhang, Yun; Wei, Hongxing; Yang, Bo

2018-04-01

To design modular robot system, Petri nets and category theory are combined and the ability of simulation of Petri net is discussed. According to category theory, the method of describing the category of components in the dynamic characteristics of the system is deduced. Moreover, a modular robot system is analyzed, which provides a verifiable description of the dynamic characteristics of the system.

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.

PubMed

Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll

2016-01-04

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

DYNAMICO, an atmospheric dynamical core for high-performance climate modeling

NASA Astrophysics Data System (ADS)

Dubos, Thomas; Meurdesoif, Yann; Spiga, Aymeric; Millour, Ehouarn; Fita, Lluis; Hourdin, Frédéric; Kageyama, Masa; Traore, Abdoul-Khadre; Guerlet, Sandrine; Polcher, Jan

2017-04-01

Institut Pierre Simon Laplace has developed a very scalable atmospheric dynamical core, DYNAMICO, based on energy-conserving finite-difference/finite volume numerics on a quasi-uniform icosahedral-hexagonal mesh. Scalability is achieved by combining hybrid MPI/OpenMP parallelism to asynchronous I/O. This dynamical core has been coupled to radiative transfer physics tailored to the atmosphere of Saturn, allowing unprecedented simulations of the climate of this giant planet. For terrestrial climate studies DYNAMICO is being integrated into the IPSL Earth System Model IPSL-CM. Preliminary aquaplanet and AMIP-style simulations yield reasonable results when compared to outputs from IPSL-CM5. The observed performance suggests that an order of magnitude may be gained with respect to IPSL-CM CMIP5 simulations either on the duration of simulations or on their resolution. Longer simulations would be of interest for the study of paleoclimate, while higher resolution could improve certain aspects of the modeled climate such as extreme events, as will be explored in the HighResMIP project. Following IPSL's strategic vision of building a unified global-regional modelling system, a fully-compressible, non-hydrostatic prototype of DYNAMICO has been developed, enabling future convection-resolving simulations. Work supported by ANR project "HEAT", grant number CE23_2014_HEAT Dubos, T., Dubey, S., Tort, M., Mittal, R., Meurdesoif, Y., and Hourdin, F.: DYNAMICO-1.0, an icosahedral hydrostatic dynamical core designed for consistency and versatility, Geosci. Model Dev., 8, 3131-3150, doi:10.5194/gmd-8-3131-2015, 2015.

Influence of ecohydrologic feedbacks from simulated crop growth on integrated regional hydrologic simulations under climate scenarios

NASA Astrophysics Data System (ADS)

van Walsum, P. E. V.; Supit, I.

2012-06-01

Hydrologic climate change modelling is hampered by climate-dependent model parameterizations. To reduce this dependency, we extended the regional hydrologic modelling framework SIMGRO to host a two-way coupling between the soil moisture model MetaSWAP and the crop growth simulation model WOFOST, accounting for ecohydrologic feedbacks in terms of radiation fraction that reaches the soil, crop coefficient, interception fraction of rainfall, interception storage capacity, and root zone depth. Except for the last, these feedbacks are dependent on the leaf area index (LAI). The influence of regional groundwater on crop growth is included via a coupling to MODFLOW. Two versions of the MetaSWAP-WOFOST coupling were set up: one with exogenous vegetation parameters, the "static" model, and one with endogenous crop growth simulation, the "dynamic" model. Parameterization of the static and dynamic models ensured that for the current climate the simulated long-term averages of actual evapotranspiration are the same for both models. Simulations were made for two climate scenarios and two crops: grass and potato. In the dynamic model, higher temperatures in a warm year under the current climate resulted in accelerated crop development, and in the case of potato a shorter growing season, thus partly avoiding the late summer heat. The static model has a higher potential transpiration; depending on the available soil moisture, this translates to a higher actual transpiration. This difference between static and dynamic models is enlarged by climate change in combination with higher CO2 concentrations. Including the dynamic crop simulation gives for potato (and other annual arable land crops) systematically higher effects on the predicted recharge change due to climate change. Crop yields from soils with poor water retention capacities strongly depend on capillary rise if moisture supply from other sources is limited. Thus, including a crop simulation model in an integrated hydrologic simulation provides a valuable addition for hydrologic modelling as well as for crop modelling.

V-SUIT Model Validation Using PLSS 1.0 Test Results

NASA Technical Reports Server (NTRS)

Olthoff, Claas

2015-01-01

The dynamic portable life support system (PLSS) simulation software Virtual Space Suit (V-SUIT) has been under development at the Technische Universitat Munchen since 2011 as a spin-off from the Virtual Habitat (V-HAB) project. The MATLAB(trademark)-based V-SUIT simulates space suit portable life support systems and their interaction with a detailed and also dynamic human model, as well as the dynamic external environment of a space suit moving on a planetary surface. To demonstrate the feasibility of a large, system level simulation like V-SUIT, a model of NASA's PLSS 1.0 prototype was created. This prototype was run through an extensive series of tests in 2011. Since the test setup was heavily instrumented, it produced a wealth of data making it ideal for model validation. The implemented model includes all components of the PLSS in both the ventilation and thermal loops. The major components are modeled in greater detail, while smaller and ancillary components are low fidelity black box models. The major components include the Rapid Cycle Amine (RCA) CO2 removal system, the Primary and Secondary Oxygen Assembly (POS/SOA), the Pressure Garment System Volume Simulator (PGSVS), the Human Metabolic Simulator (HMS), the heat exchanger between the ventilation and thermal loops, the Space Suit Water Membrane Evaporator (SWME) and finally the Liquid Cooling Garment Simulator (LCGS). Using the created model, dynamic simulations were performed using same test points also used during PLSS 1.0 testing. The results of the simulation were then compared to the test data with special focus on absolute values during the steady state phases and dynamic behavior during the transition between test points. Quantified simulation results are presented that demonstrate which areas of the V-SUIT model are in need of further refinement and those that are sufficiently close to the test results. Finally, lessons learned from the modelling and validation process are given in combination with implications for the future development of other PLSS models in V-SUIT.

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

DOE PAGES

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.; ...

2016-01-01

The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2Cu 3O 7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsiblemore » for the high-current-carrying-capacity characteristic of commercial HTS wires. Finally, our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.« less

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with < 2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.

The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2Cu 3O 7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsiblemore » for the high-current-carrying-capacity characteristic of commercial HTS wires. Finally, our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.« less

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.

Tmore » he ability of high-temperature superconductors (HSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. he development and further improvement of HS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. Here, we present a critical current analysis of a real HS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2 Cu 3 O 7 - δ . his methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsible for the high-current-carrying-capacity characteristic of commercial HS wires. Our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HS wire designs.« less

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

PubMed Central

Zuckerman, Daniel M.; Chong, Lillian T.

2018-01-01

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling—the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes—protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation. PMID:28301772

Dynamic Performance Comparison for MPPT-PV Systems using Hybrid Pspice/Matlab Simulation

NASA Astrophysics Data System (ADS)

Aouchiche, N.; Becherif, M.; HadjArab, A.; Aitcheikh, M. S.; Ramadan, H. S.; Cheknane, A.

2016-10-01

The power generated by solar photovoltaic (PV) module depends on the surrounding irradiance and temperature. This paper presents a hybrid Matlab™/Pspice™ simulation model of PV system, combined with Cadence software SLPS. The hybridization is performed in order to gain the advantages of both simulation tools such as accuracy and efficiency in both Pspice electronic circuit and Matlab™ mathematical modelling respectively. For this purpose, the PV panel and the boost converter are developed using Pspice™ and hybridized with the mathematical Matlab™ model of maximum power point method controller (MPPT) through SLPS. The main objective is verify the significance of using the proposed hybrid simulation techniques in comparing the different MPPT algorithms such as the perturbation and observation (P&O), incremental of conductance (Inc-Cond) and counter reaction voltage using pilot cell (Pilot-Cell). Various simulations are performed under different atmospheric conditions in order to evaluate the dynamic behaviour for the system under study in terms of stability, efficiency and rapidity.

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.

PubMed

Zuckerman, Daniel M; Chong, Lillian T

2017-05-22

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.

Investigation of Turbulent Entrainment-Mixing Processes With a New Particle-Resolved Direct Numerical Simulation Model

DOE PAGES

Gao, Zheng; Liu, Yangang; Li, Xiaolin; ...

2018-02-19

Here, a new particle-resolved three dimensional direct numerical simulation (DNS) model is developed that combines Lagrangian droplet tracking with the Eulerian field representation of turbulence near the Kolmogorov microscale. Six numerical experiments are performed to investigate the processes of entrainment of clear air and subsequent mixing with cloudy air and their interactions with cloud microphysics. The experiments are designed to represent different combinations of three configurations of initial cloudy area and two turbulence modes (decaying and forced turbulence). Five existing measures of microphysical homogeneous mixing degree are examined, modified, and compared in terms of their ability as a unifying measuremore » to represent the effect of various entrainment-mixing mechanisms on cloud microphysics. Also examined and compared are the conventional Damköhler number and transition scale number as a dynamical measure of different mixing mechanisms. Relationships between the various microphysical measures and dynamical measures are investigated in search for a unified parameterization of entrainment-mixing processes. The results show that even with the same cloud water fraction, the thermodynamic and microphysical properties are different, especially for the decaying cases. Further analysis confirms that despite the detailed differences in cloud properties among the six simulation scenarios, the variety of turbulent entrainment-mixing mechanisms can be reasonably represented with power-law relationships between the microphysical homogeneous mixing degrees and the dynamical measures.« less

Investigation of Turbulent Entrainment-Mixing Processes With a New Particle-Resolved Direct Numerical Simulation Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Zheng; Liu, Yangang; Li, Xiaolin

Here, a new particle-resolved three dimensional direct numerical simulation (DNS) model is developed that combines Lagrangian droplet tracking with the Eulerian field representation of turbulence near the Kolmogorov microscale. Six numerical experiments are performed to investigate the processes of entrainment of clear air and subsequent mixing with cloudy air and their interactions with cloud microphysics. The experiments are designed to represent different combinations of three configurations of initial cloudy area and two turbulence modes (decaying and forced turbulence). Five existing measures of microphysical homogeneous mixing degree are examined, modified, and compared in terms of their ability as a unifying measuremore » to represent the effect of various entrainment-mixing mechanisms on cloud microphysics. Also examined and compared are the conventional Damköhler number and transition scale number as a dynamical measure of different mixing mechanisms. Relationships between the various microphysical measures and dynamical measures are investigated in search for a unified parameterization of entrainment-mixing processes. The results show that even with the same cloud water fraction, the thermodynamic and microphysical properties are different, especially for the decaying cases. Further analysis confirms that despite the detailed differences in cloud properties among the six simulation scenarios, the variety of turbulent entrainment-mixing mechanisms can be reasonably represented with power-law relationships between the microphysical homogeneous mixing degrees and the dynamical measures.« less

Dynamical Systems in Circuit Designer's Eyes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Odyniec, M.

Examples of nonlinear circuit design are given. Focus of the design process is on theory and engineering methods (as opposed to numerical analysis). Modeling is related to measurements It is seen that the phase plane is still very useful with proper models Harmonic balance/describing function offers powerful insight (via the combination of simulation with circuit and ODE theory). Measurement and simulation capabilities increased, especially harmonics measurements (since sinusoids are easy to generate)

Testing the Applicability of Nernst-Planck Theory in Ion Channels: Comparisons with Brownian Dynamics Simulations

PubMed Central

Song, Chen; Corry, Ben

2011-01-01

The macroscopic Nernst-Planck (NP) theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD) simulations. To thoroughly test the theory in a range of situations, calculations were made in a series of simplified cylindrical channels with radii ranging from 3 to 15 Å, in a more complex ‘catenary’ channel, and in a realistic model of the mechanosensitive channel MscS. The extensive tests indicate that the NP equation is applicable in narrow ion channels provided that accurate concentrations and potentials can be input as the currents obtained from the combination of BD and NP match well with those obtained directly from BD simulations, although some discrepancies are seen when the ion concentrations are not radially uniform. This finding opens a door to utilising the results of microscopic simulations in continuum theory, something that is likely to be useful in the investigation of a range of biophysical and nano-scale applications and should stimulate further studies in this direction. PMID:21731672

Testing the applicability of Nernst-Planck theory in ion channels: comparisons with Brownian dynamics simulations.

PubMed

Song, Chen; Corry, Ben

2011-01-01

The macroscopic Nernst-Planck (NP) theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD) simulations. To thoroughly test the theory in a range of situations, calculations were made in a series of simplified cylindrical channels with radii ranging from 3 to 15 Å, in a more complex 'catenary' channel, and in a realistic model of the mechanosensitive channel MscS. The extensive tests indicate that the NP equation is applicable in narrow ion channels provided that accurate concentrations and potentials can be input as the currents obtained from the combination of BD and NP match well with those obtained directly from BD simulations, although some discrepancies are seen when the ion concentrations are not radially uniform. This finding opens a door to utilising the results of microscopic simulations in continuum theory, something that is likely to be useful in the investigation of a range of biophysical and nano-scale applications and should stimulate further studies in this direction.

Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions

PubMed Central

Zhou, Yanzi; Wang, Shenglong; Li, Yongle; Zhang, Yingkai

2016-01-01

There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics simulation (aiQM/MM-MD) with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem–Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem–Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes. PMID:27498636

Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy

PubMed Central

Voltz, Karine; Léonard, Jérémie; Touceda, Patricia Tourón; Conyard, Jamie; Chaker, Ziyad; Dejaegere, Annick; Godet, Julien; Mély, Yves; Haacke, Stefan; Stote, Roland H.

2016-01-01

Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies. PMID:26896800

Power Control and Optimization of Photovoltaic and Wind Energy Conversion Systems

NASA Astrophysics Data System (ADS)

Ghaffari, Azad

Power map and Maximum Power Point (MPP) of Photovoltaic (PV) and Wind Energy Conversion Systems (WECS) highly depend on system dynamics and environmental parameters, e.g., solar irradiance, temperature, and wind speed. Power optimization algorithms for PV systems and WECS are collectively known as Maximum Power Point Tracking (MPPT) algorithm. Gradient-based Extremum Seeking (ES), as a non-model-based MPPT algorithm, governs the system to its peak point on the steepest descent curve regardless of changes of the system dynamics and variations of the environmental parameters. Since the power map shape defines the gradient vector, then a close estimate of the power map shape is needed to create user assignable transients in the MPPT algorithm. The Hessian gives a precise estimate of the power map in a neighborhood around the MPP. The estimate of the inverse of the Hessian in combination with the estimate of the gradient vector are the key parts to implement the Newton-based ES algorithm. Hence, we generate an estimate of the Hessian using our proposed perturbation matrix. Also, we introduce a dynamic estimator to calculate the inverse of the Hessian which is an essential part of our algorithm. We present various simulations and experiments on the micro-converter PV systems to verify the validity of our proposed algorithm. The ES scheme can also be used in combination with other control algorithms to achieve desired closed-loop performance. The WECS dynamics is slow which causes even slower response time for the MPPT based on the ES. Hence, we present a control scheme, extended from Field-Oriented Control (FOC), in combination with feedback linearization to reduce the convergence time of the closed-loop system. Furthermore, the nonlinear control prevents magnetic saturation of the stator of the Induction Generator (IG). The proposed control algorithm in combination with the ES guarantees the closed-loop system robustness with respect to high level parameter uncertainty in the IG dynamics. The simulation results verify the effectiveness of the proposed algorithm.

Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method.

PubMed

Karain, Wael I

2017-11-28

Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new method that has the ability to detect transitions in dynamics based on the recurrences in the dynamical system. It combines bootstrapping and recurrence quantification analysis. We start from the assumption that a protein has a "baseline" recurrence structure over a given period of time. Any statistically significant deviation from this recurrence structure, as inferred from complexity measures provided by recurrence quantification analysis, is considered a transition in the dynamics of the protein. We apply this technique to a 132 ns long molecular dynamics simulation of the β-Lactamase Inhibitory Protein BLIP. We are able to detect conformational transitions in the nanosecond range in the recurrence dynamics of the BLIP protein during the simulation. The results compare favorably to those extracted using the principal component analysis technique. The recurrence quantification analysis based bootstrap technique is able to detect transitions between different dynamics states for a protein over different time scales. It is not limited to linear dynamics regimes, and can be generalized to any time scale. It also has the potential to be used to cluster frames in molecular dynamics trajectories according to the nature of their recurrence dynamics. One shortcoming for this method is the need to have large enough time windows to insure good statistical quality for the recurrence complexity measures needed to detect the transitions.

Dynamic simulation of the effect of soft toric contact lenses movement on retinal image quality.

PubMed

Niu, Yafei; Sarver, Edwin J; Stevenson, Scott B; Marsack, Jason D; Parker, Katrina E; Applegate, Raymond A

2008-04-01

To report the development of a tool designed to dynamically simulate the effect of soft toric contact lens movement on retinal image quality, initial findings on three eyes, and the next steps to be taken to improve the utility of the tool. Three eyes of two subjects wearing soft toric contact lenses were cyclopleged with 1% cyclopentolate and 2.5% phenylephrine. Four hundred wavefront aberration measurements over a 5-mm pupil were recorded during soft contact lens wear at 30 Hz using a complete ophthalmic analysis system aberrometer. Each wavefront error measurement was input into Visual Optics Laboratory (version 7.15, Sarver and Associates, Inc.) to generate a retinal simulation of a high contrast log MAR visual acuity chart. The individual simulations were combined into a single dynamic movie using a custom MatLab PsychToolbox program. Visual acuity was measured for each eye reading the movie with best cycloplegic spectacle correction through a 3-mm artificial pupil to minimize the influence of the eyes' uncorrected aberrations. Comparison of the simulated acuity was made to values recorded while the subject read unaberrated charts with contact lenses through a 5-mm artificial pupil. For one study eye, average acuity was the same as the natural contact lens viewing condition. For the other two study eyes visual acuity of the best simulation was more than one line worse than natural viewing conditions. Dynamic simulation of retinal image quality, although not yet perfect, is a promising technique for visually illustrating the optical effects on image quality because of the movements of alignment-sensitive corrections.

A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules

PubMed Central

Elcock, Adrian H.

2013-01-01

Inclusion of hydrodynamic interactions (HIs) is essential in simulations of biological macromolecules that treat the solvent implicitly if the macromolecules are to exhibit correct translational and rotational diffusion. The present work describes the development and testing of a simple approach aimed at allowing more rapid computation of HIs in coarse-grained Brownian dynamics simulations of systems that contain large numbers of flexible macromolecules. The method combines a complete treatment of intramolecular HIs with an approximate treatment of the intermolecular HIs which assumes that the molecules are effectively spherical; all of the HIs are calculated at the Rotne-Prager-Yamakawa level of theory. When combined with Fixman’s Chebyshev polynomial method for calculating correlated random displacements, the proposed method provides an approach that is simple to program but sufficiently fast that it makes it computationally viable to include HIs in large-scale simulations. Test calculations performed on very coarse-grained models of the pyruvate dehydrogenase (PDH) E2 complex and on oligomers of ParM (ranging in size from 1 to 20 monomers) indicate that the method reproduces the translational diffusion behavior seen in more complete HI simulations surprisingly well; the method performs less well at capturing rotational diffusion but its discrepancies diminish with increasing size of the simulated assembly. Simulations of residue-level models of two tetrameric protein models demonstrate that the method also works well when more structurally detailed models are used in the simulations. Finally, test simulations of systems containing up to 1024 coarse-grained PDH molecules indicate that the proposed method rapidly becomes more efficient than the conventional BD approach in which correlated random displacements are obtained via a Cholesky decomposition of the complete diffusion tensor. PMID:23914146

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

PubMed Central

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-01-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 PMID:26753008

Simulation study of the initial crystallization processes of poly(3-hexylthiophene) in solution: ordering dynamics of main chains and side chains.

PubMed

Takizawa, Yuumi; Shimomura, Takeshi; Miura, Toshiaki

2013-05-23

We study the initial nucleation dynamics of poly(3-hexylthiophene) (P3HT) in solution, focusing on the relationship between the ordering process of main chains and that of side chains. We carried out Langevin dynamics simulation and found that the initial nucleation processes consist of three steps: the ordering of ring orientation, the ordering of main-chain vectors, and the ordering of side chains. At the start, the normal vectors of thiophene rings aligned in a very short time, followed by alignment of main-chain end-to-end vectors. The flexible side-chain ordering took almost 5 times longer than the rigid-main-chain ordering. The simulation results indicated that the ordering of side chains was induced after the formation of the regular stack structure of main chains. This slow ordering dynamics of flexible side chains is one of the factors that cause anisotropic nuclei growth, which would be closely related to the formation of nanofiber structures without external flow field. Our simulation results revealed how the combined structure of the planar and rigid-main-chain backbones and the sparse flexible side chains lead to specific ordering behaviors that are not observed in ordinary linear polymer crystallization processes.

Dynamical role of Ekman pumping in rapidly rotating convection

NASA Astrophysics Data System (ADS)

Stellmach, Stephan; Julien, Keith; Cheng, Jonathan; Aurnou, Jonathan

2015-04-01

The exact nature of the mechanical boundary conditions (i.e. no-slip versus stress-free) is usually considered to be of secondary importance in the rapidly rotating parameter regime characterizing planetary cores. While they have considerable influence for the Ekman numbers achievable in today's global simulations, for planetary values both the viscous Ekman layers and the associated secondary flows are generally expected to become negligibly small. In fact, usually the main purpose of using stress-free boundary conditions in numerical dynamo simulations is to suppress unrealistically large friction and pumping effects. In this study, we investigate the influence of the mechanical boundary conditions on core convection systematically. By restricting ourselves to the idealized case of rapidly rotating Rayleigh-Bénard convection, we are able to combine results from direct numerical simulations (DNS), laboratory experiments and asymptotic theory into a coherent picture. Contrary to the general expectation, we show that the dynamical effects of Ekman pumping increase with decreasing Ekman number over the investigated parameter range. While stress-free DNS results converge to the asymptotic predictions, both no-slip simulations and laboratory experiments consistently reveal increasingly large deviations from the existing asymptotic theory based on dynamically passive Ekman layers. The implications of these results for core dynamics are discussed briefly.

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.

PubMed

Lei, Hongxing; Wu, Chun; Liu, Haiguang; Duan, Yong

2007-03-20

High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C(alpha)-rmsd from the x-ray structure was 0.46 A, and the C(alpha)- rmsd of the center of the most populated cluster was 1.78 A at 300 K. ab initio simulations have previously not reached this level. The folding landscape of HP35 can be partitioned into the native, denatured, and two intermediate-state regions. The native state is separated from the major folding intermediate state by a small barrier, whereas a large barrier exists between the major folding intermediate and the denatured states. The melting temperature T(m) = 339 K extracted from the heat-capacity profile was in close agreement with the experimentally derived T(m) = 342 K. A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined.

An innovative modeling approach using Qual2K and HEC-RAS integration to assess the impact of tidal effect on River Water quality simulation.

PubMed

Fan, Chihhao; Ko, Chun-Han; Wang, Wei-Shen

2009-04-01

Water quality modeling has been shown to be a useful tool in strategic water quality management. The present study combines the Qual2K model with the HEC-RAS model to assess the water quality of a tidal river in northern Taiwan. The contaminant loadings of biochemical oxygen demand (BOD), ammonia nitrogen (NH(3)-N), total phosphorus (TP), and sediment oxygen demand (SOD) are utilized in the Qual2K simulation. The HEC-RAS model is used to: (i) estimate the hydraulic constants for atmospheric re-aeration constant calculation; and (ii) calculate the water level profile variation to account for concentration changes as a result of tidal effect. The results show that HEC-RAS-assisted Qual2K simulations taking tidal effect into consideration produce water quality indices that, in general, agree with the monitoring data of the river. Comparisons of simulations with different combinations of contaminant loadings demonstrate that BOD is the most import contaminant. Streeter-Phelps simulation (in combination with HEC-RAS) is also performed for comparison, and the results show excellent agreement with the observed data. This paper is the first report of the innovative use of a combination of the HEC-RAS model and the Qual2K model (or Streeter-Phelps equation) to simulate water quality in a tidal river. The combination is shown to provide an alternative for water quality simulation of a tidal river when available dynamic-monitoring data are insufficient to assess the tidal effect of the river.

Information Processing Capacity of Dynamical Systems

NASA Astrophysics Data System (ADS)

Dambre, Joni; Verstraeten, David; Schrauwen, Benjamin; Massar, Serge

2012-07-01

Many dynamical systems, both natural and artificial, are stimulated by time dependent external signals, somehow processing the information contained therein. We demonstrate how to quantify the different modes in which information can be processed by such systems and combine them to define the computational capacity of a dynamical system. This is bounded by the number of linearly independent state variables of the dynamical system, equaling it if the system obeys the fading memory condition. It can be interpreted as the total number of linearly independent functions of its stimuli the system can compute. Our theory combines concepts from machine learning (reservoir computing), system modeling, stochastic processes, and functional analysis. We illustrate our theory by numerical simulations for the logistic map, a recurrent neural network, and a two-dimensional reaction diffusion system, uncovering universal trade-offs between the non-linearity of the computation and the system's short-term memory.

Quasielastic neutron scattering in biology: Theory and applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vural, Derya; Univ. of Tennessee, Knoxville, TN; Hu, Xiaohu

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of thismore » in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Lastly, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains.« less

Quasielastic neutron scattering in biology: Theory and applications

DOE PAGES

Vural, Derya; Univ. of Tennessee, Knoxville, TN; Hu, Xiaohu; ...

2016-06-15

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of thismore » in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Lastly, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains.« less

Information Processing Capacity of Dynamical Systems

PubMed Central

Dambre, Joni; Verstraeten, David; Schrauwen, Benjamin; Massar, Serge

2012-01-01

Many dynamical systems, both natural and artificial, are stimulated by time dependent external signals, somehow processing the information contained therein. We demonstrate how to quantify the different modes in which information can be processed by such systems and combine them to define the computational capacity of a dynamical system. This is bounded by the number of linearly independent state variables of the dynamical system, equaling it if the system obeys the fading memory condition. It can be interpreted as the total number of linearly independent functions of its stimuli the system can compute. Our theory combines concepts from machine learning (reservoir computing), system modeling, stochastic processes, and functional analysis. We illustrate our theory by numerical simulations for the logistic map, a recurrent neural network, and a two-dimensional reaction diffusion system, uncovering universal trade-offs between the non-linearity of the computation and the system's short-term memory. PMID:22816038

Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System (T-MATS)

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei (OA)

2014-01-01

A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This presentation describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this presentation is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture.

Time-Dependent Density Functional Theory for Open Systems and Its Applications.

PubMed

Chen, Shuguang; Kwok, YanHo; Chen, GuanHua

2018-02-20

Photovoltaic devices, electrochemical cells, catalysis processes, light emitting diodes, scanning tunneling microscopes, molecular electronics, and related devices have one thing in common: open quantum systems where energy and matter are not conserved. Traditionally quantum chemistry is confined to isolated and closed systems, while quantum dissipation theory studies open quantum systems. The key quantity in quantum dissipation theory is the reduced system density matrix. As the reduced system density matrix is an O(M! × M!) matrix, where M is the number of the particles of the system of interest, quantum dissipation theory can only be employed to simulate systems of a few particles or degrees of freedom. It is thus important to combine quantum chemistry and quantum dissipation theory so that realistic open quantum systems can be simulated from first-principles. We have developed a first-principles method to simulate the dynamics of open electronic systems, the time-dependent density functional theory for open systems (TDDFT-OS). Instead of the reduced system density matrix, the key quantity is the reduced single-electron density matrix, which is an N × N matrix where N is the number of the atomic bases of the system of interest. As the dimension of the key quantity is drastically reduced, the TDDFT-OS can thus be used to simulate the dynamics of realistic open electronic systems and efficient numerical algorithms have been developed. As an application, we apply the method to study how quantum interference develops in a molecular transistor in time domain. We include electron-phonon interaction in our simulation and show that quantum interference in the given system is robust against nuclear vibration not only in the steady state but also in the transient dynamics. As another application, by combining TDDFT-OS with Ehrenfest dynamics, we study current-induced dissociation of water molecules under scanning tunneling microscopy and follow its time dependent dynamics. Given the rapid development in ultrafast experiments with atomic resolution in recent years, time dependent simulation of open electronic systems will be useful to gain insight and understanding of such experiments. This Account will mainly focus on the practical aspects of the TDDFT-OS method, describing the numerical implementation and demonstrating the method with applications.

Exploring the Dynamics of Exoplanetary Systems in a Young Stellar Cluster

NASA Astrophysics Data System (ADS)

Thornton, Jonathan Daniel; Glaser, Joseph Paul; Wall, Joshua Edward

2018-01-01

I describe a dynamical simulation of planetary systems in a young star cluster. One rather arbitrary aspect of cluster simulations is the choice of initial conditions. These are typically chosen from some standard model, such as Plummer or King, or from a “fractal” distribution to try to model young clumpy systems. Here I adopt the approach of realizing an initial cluster model directly from a detailed magnetohydrodynamical model of cluster formation from a 1000-solar-mass interstellar gas cloud, with magnetic fields and radiative and wind feedback from massive stars included self-consistently. The N-body simulation of the stars and planets starts once star formation is largely over and feedback has cleared much of the gas from the region where the newborn stars reside. It continues until the cluster dissolves in the galactic field. Of particular interest is what would happen to the free-floating planets created in the gas cloud simulation. Are they captured by a star or are they ejected from the cluster? This method of building a dynamical cluster simulation directly from the results of a cluster formation model allows us to better understand the evolution of young star clusters and enriches our understanding of extrasolar planet development in them. These simulations were performed within the AMUSE simulation framework, and combine N-body, multiples and background potential code.

Combined 3D-QSAR, molecular docking, molecular dynamics simulation, and binding free energy calculation studies on the 5-hydroxy-2H-pyridazin-3-one derivatives as HCV NS5B polymerase inhibitors.

PubMed

Yu, Haijing; Fang, Yu; Lu, Xia; Liu, Yongjuan; Zhang, Huabei

2014-01-01

The NS5B RNA-dependent RNA polymerase (RdRP) is a promising therapeutic target for developing novel anti-hepatitis C virus (HCV) drugs. In this work, a combined molecular modeling study was performed on a series of 193 5-hydroxy-2H-pyridazin-3-one derivatives as inhibitors of HCV NS5B Polymerase. The best 3D-QSAR models, including CoMFA and CoMSIA, are based on receptor (or docking). Furthermore, a 40-ns molecular dynamics (MD) simulation and binding free energy calculations using docked structures of NS5B with ten compounds, which have diverse structures and pIC50 values, were employed to determine the detailed binding process and to compare the binding modes of the inhibitors with different activities. On one side, the stability and rationality of molecular docking and 3D-QSAR results were validated by MD simulation. The binding free energies calculated by the MM-PBSA method gave a good correlation with the experimental biological activity. On the other side, by analyzing some differences between the molecular docking and the MD simulation results, we can find that the MD simulation could also remedy the defects of molecular docking. The analyses of the combined molecular modeling results have identified that Tyr448, Ser556, and Asp318 are the key amino acid residues in the NS5B binding pocket. The results from this study can provide some insights into the development of novel potent NS5B inhibitors. © 2013 John Wiley & Sons A/S.

Three Dimensional Numerical Simulation of Rocket-based Combined-cycle Engine Response During Mode Transition Events

NASA Technical Reports Server (NTRS)

Edwards, Jack R.; McRae, D. Scott; Bond, Ryan B.; Steffan, Christopher (Technical Monitor)

2003-01-01

The GTX program at NASA Glenn Research Center is designed to develop a launch vehicle concept based on rocket-based combined-cycle (RBCC) propulsion. Experimental testing, cycle analysis, and computational fluid dynamics modeling have all demonstrated the viability of the GTX concept, yet significant technical issues and challenges still remain. Our research effort develops a unique capability for dynamic CFD simulation of complete high-speed propulsion devices and focuses this technology toward analysis of the GTX response during critical mode transition events. Our principal attention is focused on Mode 1/Mode 2 operation, in which initial rocket propulsion is transitioned into thermal-throat ramjet propulsion. A critical element of the GTX concept is the use of an Independent Ramjet Stream (IRS) cycle to provide propulsion at Mach numbers less than 3. In the IRS cycle, rocket thrust is initially used for primary power, and the hot rocket plume is used as a flame-holding mechanism for hydrogen fuel injected into the secondary air stream. A critical aspect is the establishment of a thermal throat in the secondary stream through the combination of area reduction effects and combustion-induced heat release. This is a necessity to enable the power-down of the rocket and the eventual shift to ramjet mode. Our focus in this first year of the grant has been in three areas, each progressing directly toward the key initial goal of simulating thermal throat formation during the IRS cycle: CFD algorithm development; simulation of Mode 1 experiments conducted at Glenn's Rig 1 facility; and IRS cycle simulations. The remainder of this report discusses each of these efforts in detail and presents a plan of work for the next year.

Direct dynamics simulation of the impact phase in heel-toe running.

PubMed

Gerritsen, K G; van den Bogert, A J; Nigg, B M

1995-06-01

The influence of muscle activation, position and velocities of body segments at touchdown and surface properties on impact forces during heel-toe running was investigated using a direct dynamics simulation technique. The runner was represented by a two-dimensional four- (rigid body) segment musculo-skeletal model. Incorporated into the muscle model were activation dynamics, force-length and force-velocity characteristics of seven major muscle groups of the lower extremities: mm. glutei, hamstrings, m. rectus femoris, mm. vasti, m. gastrocnemius, m. soleus and m. tibialis anterior. The vertical force-deformation characteristics of heel, shoe and ground were modeled by a non-linear visco-elastic element. The maximum of a typical simulated impact force was 1.6 times body weight. The influence of muscle activation was examined by generating muscle stimulation combinations which produce the same (experimentally determined) resultant joint moments at heelstrike. Simulated impact peak forces with these different combinations of muscle stimulation levels varied less than 10%. Without this restriction on initial joint moments, muscle activation had potentially a much larger effect on impact force. Impact peak force was to a great extent influenced by plantar flexion (85 N per degree of change in foot angle) and vertical velocity of the heel (212 N per 0.1 m s-1 change in velocity) at touchdown. Initial knee flexion (68 N per degree of change in leg angle) also played a role in the absorption of impact. Increased surface stiffness resulted in higher impact peak forces (60 N mm-1 decrease in deformation).(ABSTRACT TRUNCATED AT 250 WORDS)

Dynamic rupture scenarios from Sumatra to Iceland - High-resolution earthquake source physics on natural fault systems

NASA Astrophysics Data System (ADS)

Gabriel, A. A.; Madden, E. H.; Ulrich, T.; Wollherr, S.

2016-12-01

Capturing the observed complexity of earthquake sources in dynamic rupture simulations may require: non-linear fault friction, thermal and fluid effects, heterogeneous fault stress and strength initial conditions, fault curvature and roughness, on- and off-fault non-elastic failure. All of these factors have been independently shown to alter dynamic rupture behavior and thus possibly influence the degree of realism attainable via simulated ground motions. In this presentation we will show examples of high-resolution earthquake scenarios, e.g. based on the 2004 Sumatra-Andaman Earthquake and a potential rupture of the Husavik-Flatey fault system in Northern Iceland. The simulations combine a multitude of representations of source complexity at the necessary spatio-temporal resolution enabled by excellent scalability on modern HPC systems. Such simulations allow an analysis of the dominant factors impacting earthquake source physics and ground motions given distinct tectonic settings or distinct focuses of seismic hazard assessment. Across all simulations, we find that fault geometry concurrently with the regional background stress state provide a first order influence on source dynamics and the emanated seismic wave field. The dynamic rupture models are performed with SeisSol, a software package based on an ADER-Discontinuous Galerkin scheme for solving the spontaneous dynamic earthquake rupture problem with high-order accuracy in space and time. Use of unstructured tetrahedral meshes allows for a realistic representation of the non-planar fault geometry, subsurface structure and bathymetry. The results presented highlight the fact that modern numerical methods are essential to further our understanding of earthquake source physics and complement both physic-based ground motion research and empirical approaches in seismic hazard analysis.

Dynamic rupture scenarios from Sumatra to Iceland - High-resolution earthquake source physics on natural fault systems

NASA Astrophysics Data System (ADS)

Gabriel, Alice-Agnes; Madden, Elizabeth H.; Ulrich, Thomas; Wollherr, Stephanie

2017-04-01

Capturing the observed complexity of earthquake sources in dynamic rupture simulations may require: non-linear fault friction, thermal and fluid effects, heterogeneous fault stress and fault strength initial conditions, fault curvature and roughness, on- and off-fault non-elastic failure. All of these factors have been independently shown to alter dynamic rupture behavior and thus possibly influence the degree of realism attainable via simulated ground motions. In this presentation we will show examples of high-resolution earthquake scenarios, e.g. based on the 2004 Sumatra-Andaman Earthquake, the 1994 Northridge earthquake and a potential rupture of the Husavik-Flatey fault system in Northern Iceland. The simulations combine a multitude of representations of source complexity at the necessary spatio-temporal resolution enabled by excellent scalability on modern HPC systems. Such simulations allow an analysis of the dominant factors impacting earthquake source physics and ground motions given distinct tectonic settings or distinct focuses of seismic hazard assessment. Across all simulations, we find that fault geometry concurrently with the regional background stress state provide a first order influence on source dynamics and the emanated seismic wave field. The dynamic rupture models are performed with SeisSol, a software package based on an ADER-Discontinuous Galerkin scheme for solving the spontaneous dynamic earthquake rupture problem with high-order accuracy in space and time. Use of unstructured tetrahedral meshes allows for a realistic representation of the non-planar fault geometry, subsurface structure and bathymetry. The results presented highlight the fact that modern numerical methods are essential to further our understanding of earthquake source physics and complement both physic-based ground motion research and empirical approaches in seismic hazard analysis.

String model for the dynamics of glass-forming liquids

PubMed Central

Pazmiño Betancourt, Beatriz A.; Douglas, Jack F.; Starr, Francis W.

2014-01-01

We test the applicability of a living polymerization theory to describe cooperative string-like particle rearrangement clusters (strings) observed in simulations of a coarse-grained polymer melt. The theory quantitatively describes the interrelation between the average string length L, configurational entropy Sconf, and the order parameter for string assembly Φ without free parameters. Combining this theory with the Adam-Gibbs model allows us to predict the relaxation time τ in a lower temperature T range than accessible by current simulations. In particular, the combined theories suggest a return to Arrhenius behavior near Tg and a low T residual entropy, thus avoiding a Kauzmann “entropy crisis.” PMID:24880303

String model for the dynamics of glass-forming liquids.

PubMed

Pazmiño Betancourt, Beatriz A; Douglas, Jack F; Starr, Francis W

2014-05-28

We test the applicability of a living polymerization theory to describe cooperative string-like particle rearrangement clusters (strings) observed in simulations of a coarse-grained polymer melt. The theory quantitatively describes the interrelation between the average string length L, configurational entropy Sconf, and the order parameter for string assembly Φ without free parameters. Combining this theory with the Adam-Gibbs model allows us to predict the relaxation time τ in a lower temperature T range than accessible by current simulations. In particular, the combined theories suggest a return to Arrhenius behavior near Tg and a low T residual entropy, thus avoiding a Kauzmann "entropy crisis."

Dynamic Snap-Through of Thin-Walled Structures by a Reduced Order Method

NASA Technical Reports Server (NTRS)

Przekop, Adam; Rizzi, Stephen A.

2006-01-01

The goal of this investigation is to further develop nonlinear modal numerical simulation methods for application to geometrically nonlinear response of structures exposed to combined high intensity random pressure fluctuations and thermal loadings. The study is conducted on a flat aluminum beam, which permits a comparison of results obtained by a reduced-order analysis with those obtained from a numerically intensive simulation in physical degrees-of-freedom. A uniformly distributed thermal loading is first applied to investigate the dynamic instability associated with thermal buckling. A uniformly distributed random loading is added to investigate the combined thermal-acoustic response. In the latter case, three types of response characteristics are considered, namely: (i) small amplitude vibration around one of the two stable buckling equilibrium positions, (ii) intermittent snap-through response between the two equilibrium positions, and (iii) persistent snap-through response between the two equilibrium positions. For the reduced order analysis, four categories of modal basis functions are identified including those having symmetric transverse (ST), anti-symmetric transverse (AT), symmetric in-plane (SI), and anti-symmetric in-plane (AI) displacements. The effect of basis selection on the quality of results is investigated for the dynamic thermal buckling and combined thermal-acoustic response. It is found that despite symmetric geometry, loading, and boundary conditions, the AT and SI modes must be included in the basis as they participate in the snap-through behavior.

Dynamic Snap-Through of Thermally Buckled Structures by a Reduced Order Method

NASA Technical Reports Server (NTRS)

Przekop, Adam; Rizzi, Stephen A.

2007-01-01

The goal of this investigation is to further develop nonlinear modal numerical simulation methods for application to geometrically nonlinear response of structures exposed to combined high intensity random pressure fluctuations and thermal loadings. The study is conducted on a flat aluminum beam, which permits a comparison of results obtained by a reduced-order analysis with those obtained from a numerically intensive simulation in physical degrees-of-freedom. A uniformly distributed thermal loading is first applied to investigate the dynamic instability associated with thermal buckling. A uniformly distributed random loading is added to investigate the combined thermal-acoustic response. In the latter case, three types of response characteristics are considered, namely: (i) small amplitude vibration around one of the two stable buckling equilibrium positions, (ii) intermittent snap-through response between the two equilibrium positions, and (iii) persistent snap-through response between the two equilibrium positions. For the reduced-order analysis, four categories of modal basis functions are identified including those having symmetric transverse, anti-symmetric transverse, symmetric in-plane, and anti-symmetric in-plane displacements. The effect of basis selection on the quality of results is investigated for the dynamic thermal buckling and combined thermal-acoustic response. It is found that despite symmetric geometry, loading, and boundary conditions, the anti-symmetric transverse and symmetric in-plane modes must be included in the basis as they participate in the snap-through behavior.

Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6

NASA Astrophysics Data System (ADS)

Dai, Yawei; Seeger, Markus; Weng, Jingwei; Song, Song; Wang, Wenning; Tan, Yan-Wen

2016-08-01

Cellular informational and metabolic processes are propagated with specific membrane fusions governed by soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNARE). SNARE protein Ykt6 is highly expressed in brain neurons and plays a critical role in the membrane-trafficking process. Studies suggested that Ykt6 undergoes a conformational change at the interface between its longin domain and the SNARE core. In this work, we study the conformational state distributions and dynamics of rat Ykt6 by means of single-molecule Förster Resonance Energy Transfer (smFRET) and Fluorescence Cross-Correlation Spectroscopy (FCCS). We observed that intramolecular conformational dynamics between longin domain and SNARE core occurred at the timescale ~200 μs. Furthermore, this dynamics can be regulated and even eliminated by the presence of lipid dodecylphoshpocholine (DPC). Our molecular dynamic (MD) simulations have shown that, the SNARE core exhibits a flexible structure while the longin domain retains relatively stable in apo state. Combining single molecule experiments and theoretical MD simulations, we are the first to provide a quantitative dynamics of Ykt6 and explain the functional conformational change from a qualitative point of view.

Coupled turbulence and aerosol dynamics modeling of vehicle exhaust plumes using the CTAG model

NASA Astrophysics Data System (ADS)

Wang, Yan Jason; Zhang, K. Max

2012-11-01

This paper presents the development and evaluation of an environmental turbulent reacting flow model, the Comprehensive Turbulent Aerosol Dynamics and Gas Chemistry (CTAG) model. CTAG is designed to simulate transport and transformation of multiple air pollutants, e.g., from emission sources to ambient background. For the on-road and near-road applications, CTAG explicitly couples the major turbulent mixing processes, i.e., vehicle-induced turbulence (VIT), road-induced turbulence (RIT) and atmospheric boundary layer turbulence with gas-phase chemistry and aerosol dynamics. CTAG's transport model is referred to as CFD-VIT-RIT. This paper presents the evaluation of the CTAG model in simulating the dynamics of individual plumes in the “tailpipe-to-road” stage, i.e., VIT behind a moving van and aerosol dynamics in the wake of a diesel car by comparing the modeling results against the respective field measurements. Combined with sensitivity studies, we analyze the relative roles of VIT, sulfuric acid induced nucleation, condensation of organic compounds and presence of soot-mode particles in capturing the dynamics of exhaust plumes as well as their implications in vehicle emission controls.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB.

PubMed

Mansouri, Misagh; Reinbolt, Jeffrey A

2012-05-11

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB's variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1s (OpenSim) to 2.9s (MATLAB). For the closed-loop case, a proportional-integral-derivative controller was used to successfully balance a pole on model's hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB

PubMed Central

Mansouri, Misagh; Reinbolt, Jeffrey A.

2013-01-01

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB’s variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1 s (OpenSim) to 2.9 s (MATLAB). For the closed-loop case, a proportional–integral–derivative controller was used to successfully balance a pole on model’s hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. PMID:22464351

Survival and synergistic growth of mixed cultures of bifidobacteria and lactobacilli combined with prebiotic oligosaccharides in a gastrointestinal tract simulator

PubMed Central

Adamberg, Signe; Sumeri, Ingrid; Uusna, Riin; Ambalam, Padma; Kondepudi, Kanthi Kiran; Adamberg, Kaarel; Wadström, Torkel; Ljungh, Åsa

2014-01-01

Background Probiotics, especially in combination with non-digestible oligosaccharides, may balance the gut microflora while multistrain preparations may express an improved functionality over single strain cultures. In vitro gastrointestinal models enable to test survival and growth dynamics of mixed strain probiotics in a controlled, replicable manner. Methods The robustness and compatibility of multistrain probiotics composed of bifidobacteria and lactobacilli combined with mixed prebiotics (galacto-, fructo- and xylo-oligosaccharides or galactooligosaccharides and soluble starch) were studied using a dynamic gastrointestinal tract simulator (GITS). The exposure to acid and bile of the upper gastrointestinal tract was followed by dilution with a continuous decrease of the dilution rate (de-celerostat) to simulate the descending nutrient availability of the large intestine. The bacterial numbers and metabolic products were analyzed and the growth parameters determined. Results The most acid- and bile-resistant strains were Lactobacillus plantarum F44 and L. paracasei F8. Bifidobacterium breve 46 had the highest specific growth rate and, although sensitive to bile exposure, recovered during the dilution phase in most experiments. B. breve 46, L. plantarum F44, and L. paracasei F8 were selected as the most promising strains for further studies. Conclusions De-celerostat cultivation can be applied to study the mixed bacterial cultures under defined conditions of decreasing nutrient availability to select a compatible set of strains. PMID:25045346

Theoretical study of sum-frequency vibrational spectroscopy on limonene surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Ren-Hui, E-mail: zrh@iccas.ac.cn; Liu, Hao; Jing, Yuan-Yuan

2014-03-14

By combining molecule dynamics (MD) simulation and quantum chemistry computation, we calculate the surface sum-frequency vibrational spectroscopy (SFVS) of R-limonene molecules at the gas-liquid interface for SSP, PPP, and SPS polarization combinations. The distributions of the Euler angles are obtained using MD simulation, the ψ-distribution is between isotropic and Gaussian. Instead of the MD distributions, different analytical distributions such as the δ-function, Gaussian and isotropic distributions are applied to simulate surface SFVS. We find that different distributions significantly affect the absolute SFVS intensity and also influence on relative SFVS intensity, and the δ-function distribution should be used with caution whenmore » the orientation distribution is broad. Furthermore, the reason that the SPS signal is weak in reflected arrangement is discussed.« less

Theoretical approaches for dynamical ordering of biomolecular systems.

PubMed

Okumura, Hisashi; Higashi, Masahiro; Yoshida, Yuichiro; Sato, Hirofumi; Akiyama, Ryo

2018-02-01

Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Hydration of Li+ -ion in atom-bond electronegativity equalization method-7P water: a molecular dynamics simulation study.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-02-22

We have carried out molecular dynamics simulations of a Li(+) ion in water over a wide range of temperature (from 248 to 368 K). The simulations make use of the atom-bond electronegativity equalization method-7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li(+)-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li(+)-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li(+)-water potentials, successfully applied to ionic clusters Li(+)(H(2)O)(n)(n=1-6,8), are further investigated in an aqueous solution of Li(+) in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter k(lp,H)(R(lp,H)) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li(+), are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li(+)-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement with experiments and other molecular dynamics simulations on similar system.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stiegler, Thomas; Sadus, Richard J., E-mail: rsadus@swin.edu.au

General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic propertiesmore » predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.« less

Integrating viscoelastic mass spring dampers into position-based dynamics to simulate soft tissue deformation in real time

PubMed Central

Lu, Yuhua; Liu, Qian

2018-01-01

We propose a novel method to simulate soft tissue deformation for virtual surgery applications. The method considers the mechanical properties of soft tissue, such as its viscoelasticity, nonlinearity and incompressibility; its speed, stability and accuracy also meet the requirements for a surgery simulator. Modifying the traditional equation for mass spring dampers (MSD) introduces nonlinearity and viscoelasticity into the calculation of elastic force. Then, the elastic force is used in the constraint projection step for naturally reducing constraint potential. The node position is enforced by the combined spring force and constraint conservative force through Newton's second law. We conduct a comparison study of conventional MSD and position-based dynamics for our new integrating method. Our approach enables stable, fast and large step simulation by freely controlling visual effects based on nonlinearity, viscoelasticity and incompressibility. We implement a laparoscopic cholecystectomy simulator to demonstrate the practicality of our method, in which liver and gallbladder deformation can be simulated in real time. Our method is an appropriate choice for the development of real-time virtual surgery applications. PMID:29515870

Integrating viscoelastic mass spring dampers into position-based dynamics to simulate soft tissue deformation in real time.

PubMed

Xu, Lang; Lu, Yuhua; Liu, Qian

2018-02-01

We propose a novel method to simulate soft tissue deformation for virtual surgery applications. The method considers the mechanical properties of soft tissue, such as its viscoelasticity, nonlinearity and incompressibility; its speed, stability and accuracy also meet the requirements for a surgery simulator. Modifying the traditional equation for mass spring dampers (MSD) introduces nonlinearity and viscoelasticity into the calculation of elastic force. Then, the elastic force is used in the constraint projection step for naturally reducing constraint potential. The node position is enforced by the combined spring force and constraint conservative force through Newton's second law. We conduct a comparison study of conventional MSD and position-based dynamics for our new integrating method. Our approach enables stable, fast and large step simulation by freely controlling visual effects based on nonlinearity, viscoelasticity and incompressibility. We implement a laparoscopic cholecystectomy simulator to demonstrate the practicality of our method, in which liver and gallbladder deformation can be simulated in real time. Our method is an appropriate choice for the development of real-time virtual surgery applications.

Modeling and Characterization of Dynamic Failure of Soda-lime Glass Under High Speed Impact

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Wenning N.; Sun, Xin; Chen, Weinong W.

2012-05-27

In this paper, the impact-induced dynamic failure of a soda-lime glass block is studied using an integrated experimental/analytical approach. The Split Hopkinson Pressure Bar (SHPB) technique is used to conduct dynamic failure test of soda-lime glass first. The damage growth patterns and stress histories are reported for various glass specimen designs. Making use of a continuum damage mechanics (CDM)-based constitutive model, the initial failure and subsequent stiffness reduction of glass are simulated and investigated. Explicit finite element analyses are used to simulate the glass specimen impact event. A maximum shear stress-based damage evolution law is used in describing the glassmore » damage process under combined compression/shear loading. The impact test results are used to quantify the critical shear stress for the soda-lime glass under examination.« less

Seasonal variability of atmospheric tides in the mesosphere and lower thermosphere: meteor radar data and simulations

NASA Astrophysics Data System (ADS)

Pokhotelov, Dimitry; Becker, Erich; Stober, Gunter; Chau, Jorge L.

2018-06-01

Thermal tides play an important role in the global atmospheric dynamics and provide a key mechanism for the forcing of thermosphere-ionosphere dynamics from below. A method for extracting tidal contributions, based on the adaptive filtering, is applied to analyse multi-year observations of mesospheric winds from ground-based meteor radars located in northern Germany and Norway. The observed seasonal variability of tides is compared to simulations with the Kühlungsborn Mechanistic Circulation Model (KMCM). It is demonstrated that the model provides reasonable representation of the tidal amplitudes, though substantial differences from observations are also noticed. The limitations of applying a conventionally coarse-resolution model in combination with parametrisation of gravity waves are discussed. The work is aimed towards the development of an ionospheric model driven by the dynamics of the KMCM.

Linking Well-Tempered Metadynamics Simulations with Experiments

PubMed Central

Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele

2010-01-01

Abstract Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data. PMID:20441734

Hetero-diffusion of Au epitaxy on stepped Ag(110) surface: Study of the jump rate and diffusion coefficient

NASA Astrophysics Data System (ADS)

Benlattar, M.; El koraychy, E.; Kotri, A.; Mazroui, M.

2017-12-01

We have used molecular dynamics simulations combined with an interatomic potential derived from the embedded atom method, to investigate the hetero-diffusion of Au adatom near a stepped Ag(110) surface with the height of one monoatomic layer. The activation energies for different diffusion processes, which occur on the terrace and near the step edge, are calculated both by molecular statics and molecular dynamics simulations. Static energies are found by the drag method, whereas the dynamic barriers are computed at high temperature from the Arrhenius plots. Our numerical results reveal that the jump process requires very high activation energy compared to the exchange process either on the terrace or near the step edge. In this work, other processes, such as upward and downward diffusion at step edges, have also been discussed.

Combining EPR spectroscopy and X-ray crystallography to elucidate the structure and dynamics of conformationally constrained spin labels in T4 lysozyme single crystals.

PubMed

Consentius, Philipp; Gohlke, Ulrich; Loll, Bernhard; Alings, Claudia; Heinemann, Udo; Wahl, Markus C; Risse, Thomas

2017-08-09

Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling is used to investigate the structure and dynamics of conformationally constrained spin labels in T4 lysozyme single crystals. Within a single crystal, the oriented ensemble of spin bearing moieties results in a strong angle dependence of the EPR spectra. A quantitative description of the EPR spectra requires the determination of the unit cell orientation with respect to the sample tube and the orientation of the spin bearing moieties within the crystal lattice. Angle dependent EPR spectra were analyzed by line shape simulations using the stochastic Liouville equation approach developed by Freed and co-workers and an effective Hamiltonian approach. The gain in spectral information obtained from the EPR spectra of single crystalline samples taken at different frequencies, namely the X-band and Q-band, allows us to discriminate between motional models describing the spectra of isotropic solutions similarly well. In addition, it is shown that the angle dependent single crystal spectra allow us to identify two spin label rotamers with very similar side chain dynamics. These results demonstrate the utility of single crystal EPR spectroscopy in combination with spectral line shape simulation techniques to extract valuable dynamic information not readily available from the analysis of isotropic systems. In addition, it will be shown that the loss of electron density in high resolution diffraction experiments at room temperature does not allow us to conclude that there is significant structural disorder in the system.

DSMC simulations of the Shuttle Plume Impingement Flight EXperiment(SPIFEX)

NASA Technical Reports Server (NTRS)

Stewart, Benedicte; Lumpkin, Forrest

2017-01-01

During orbital maneuvers and proximity operations, a spacecraft fires its thrusters inducing plume impingement loads, heating and contamination to itself and to any other nearby spacecraft. These thruster firings are generally modeled using a combination of Computational Fluid Dynamics (CFD) and DSMC simulations. The Shuttle Plume Impingement Flight EXperiment(SPIFEX) produced data that can be compared to a high fidelity simulation. Due to the size of the Shuttle thrusters this problem was too resource intensive to be solved with DSMC when the experiment flew in 1994.

Stimulated Raman signals at conical intersections: Ab initio surface hopping simulation protocol with direct propagation of the nuclear wave function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kowalewski, Markus, E-mail: mkowalew@uci.edu; Mukamel, Shaul, E-mail: smukamel@uci.edu

2015-07-28

Femtosecond Stimulated Raman Spectroscopy (FSRS) signals that monitor the excited state conical intersections dynamics of acrolein are simulated. An effective time dependent Hamiltonian for two C—H vibrational marker bands is constructed on the fly using a local mode expansion combined with a semi-classical surface hopping simulation protocol. The signals are obtained by a direct forward and backward propagation of the vibrational wave function on a numerical grid. Earlier work is extended to fully incorporate the anharmonicities and intermode couplings.

Adaptive multiple super fast simulated annealing for stochastic microstructure reconstruction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryu, Seun; Lin, Guang; Sun, Xin

2013-01-01

Fast image reconstruction from statistical information is critical in image fusion from multimodality chemical imaging instrumentation to create high resolution image with large domain. Stochastic methods have been used widely in image reconstruction from two point correlation function. The main challenge is to increase the efficiency of reconstruction. A novel simulated annealing method is proposed for fast solution of image reconstruction. Combining the advantage of very fast cooling schedules, dynamic adaption and parallelization, the new simulation annealing algorithm increases the efficiencies by several orders of magnitude, making the large domain image fusion feasible.

Dynamic aspects of antibody:oligosaccharide complexes characterized by molecular dynamics simulations and saturation transfer difference nuclear magnetic resonance.

PubMed

Theillet, François-Xavier; Frank, Martin; Vulliez-Le Normand, Brigitte; Simenel, Catherine; Hoos, Sylviane; Chaffotte, Alain; Bélot, Frédéric; Guerreiro, Catherine; Nato, Farida; Phalipon, Armelle; Mulard, Laurence A; Delepierre, Muriel

2011-12-01

Carbohydrates are likely to maintain significant conformational flexibility in antibody (Ab):carbohydrate complexes. As demonstrated herein for the protective monoclonal Ab (mAb) F22-4 recognizing the Shigella flexneri 2a O-antigen (O-Ag) and numerous synthetic oligosaccharide fragments thereof, the combination of molecular dynamics simulations and nuclear magnetic resonance saturation transfer difference experiments, supported by physicochemical analysis, allows us to determine the binding epitope and its various contributions to affinity without using any modified oligosaccharides. Moreover, the methods used provide insights into ligand flexibility in the complex, thus enabling a better understanding of the Ab affinities observed for a representative set of synthetic O-Ag fragments. Additionally, these complementary pieces of information give evidence to the ability of the studied mAb to recognize internal as well as terminal epitopes of its cognate polysaccharide antigen. Hence, we show that an appropriate combination of computational and experimental methods provides a basis to explore carbohydrate functional mimicry and receptor binding. The strategy may facilitate the design of either ligands or carbohydrate recognition domains, according to needed improvements of the natural carbohydrate:receptor properties. © The Author 2011. Published by Oxford University Press. All rights reserved.

Modelling of Dynamic Rock Fracture Process with a Rate-Dependent Combined Continuum Damage-Embedded Discontinuity Model Incorporating Microstructure

NASA Astrophysics Data System (ADS)

Saksala, Timo

2016-10-01

This paper deals with numerical modelling of rock fracture under dynamic loading. For this end, a combined continuum damage-embedded discontinuity model is applied in finite element modelling of crack propagation in rock. In this model, the strong loading rate sensitivity of rock is captured by the rate-dependent continuum scalar damage model that controls the pre-peak nonlinear hardening part of rock behaviour. The post-peak exponential softening part of the rock behaviour is governed by the embedded displacement discontinuity model describing the mode I, mode II and mixed mode fracture of rock. Rock heterogeneity is incorporated in the present approach by random description of the rock mineral texture based on the Voronoi tessellation. The model performance is demonstrated in numerical examples where the uniaxial tension and compression tests on rock are simulated. Finally, the dynamic three-point bending test of a semicircular disc is simulated in order to show that the model correctly predicts the strain rate-dependent tensile strengths as well as the failure modes of rock in this test. Special emphasis is laid on modelling the loading rate sensitivity of tensile strength of Laurentian granite.

Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

Application of molecular dynamics simulation to predict the compatability between water-insoluble drugs and self-associating poly(ethylene oxide)-b-poly(epsilon-caprolactone) block copolymers.

PubMed

Patel, Sarthak; Lavasanifar, Afsaneh; Choi, Phillip

2008-11-01

In the present work, molecular dynamics (MD) simulation was applied to study the solubility of two water-insoluble drugs, fenofibrate and nimodipine, in a series of micelle-forming PEO-b-PCL block copolymers with combinations of blocks having different molecular weights. The solubility predictions based on the MD results were then compared with those obtained from solubility experiments and by the commonly used group contribution method (GCM). The results showed that Flory-Huggins interaction parameters computed by the MD simulations are consistent with the solubility data of the drug/PEO-b-PCL systems, whereas those calculated by the GCM significantly deviate from the experimental observation. We have also accounted for the possibility of drug solubilization in the PEO block of PEO-b-PCL.

Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mester, Zoltan; Panagiotopoulos, Athanassios Z., E-mail: azp@princeton.edu

The mean ionic activity coefficients of aqueous NaCl solutions of varying concentrations at 298.15 K and 1 bar have been obtained from molecular dynamics simulations by gradually turning on the interactions of an ion pair inserted into the solution. Several common non-polarizable water and ion models have been used in the simulations. Gibbs-Duhem equation calculations of the thermodynamic activity of water are used to confirm the thermodynamic consistency of the mean ionic activity coefficients. While the majority of model combinations predict the correct trends in mean ionic activity coefficients, they overestimate their values at high salt concentrations. The solubility predictionsmore » also suffer from inaccuracies, with all models underpredicting the experimental values, some by large factors. These results point to the need for further ion and water model development.« less

Equilibration and analysis of first-principles molecular dynamics simulations of water

NASA Astrophysics Data System (ADS)

Dawson, William; Gygi, François

2018-03-01

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Equilibration and analysis of first-principles molecular dynamics simulations of water.

PubMed

Dawson, William; Gygi, François

2018-03-28

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Intensify dodecylamine adsorption on magnesite and dolomite surfaces by monohydric alcohols

NASA Astrophysics Data System (ADS)

Zhang, Hao; Liu, Wengang; Han, Cong; Wei, Dezhou

2018-06-01

The flotation of magnesite and dolomite were investigated with the presence of single dodecylamine (DDA) and combined mixtures of DDA and monohydric alcohols, respectively. The adsorption behavior of DDA, butanol, hexanol and octanol on the surface of the two minerals were shown by molecular dynamics simulation, and the results were corresponding with the analysis of zeta potential, measurements of the contact angle and adsorption. Flotation results indicated that part of DDA could be replaced by the three alcohols (butanol, hexanol, octanol) to get better flotation results. Molecular dynamics simulation and the results of zeta potential and contact angle measurements indicated that adsorption of DDA on mineral surfaces could be strengthened by monohydric alcohols.

Qubit Architecture with High Coherence and Fast Tunable Coupling.

PubMed

Chen, Yu; Neill, C; Roushan, P; Leung, N; Fang, M; Barends, R; Kelly, J; Campbell, B; Chen, Z; Chiaro, B; Dunsworth, A; Jeffrey, E; Megrant, A; Mutus, J Y; O'Malley, P J J; Quintana, C M; Sank, D; Vainsencher, A; Wenner, J; White, T C; Geller, Michael R; Cleland, A N; Martinis, John M

2014-11-28

We introduce a superconducting qubit architecture that combines high-coherence qubits and tunable qubit-qubit coupling. With the ability to set the coupling to zero, we demonstrate that this architecture is protected from the frequency crowding problems that arise from fixed coupling. More importantly, the coupling can be tuned dynamically with nanosecond resolution, making this architecture a versatile platform with applications ranging from quantum logic gates to quantum simulation. We illustrate the advantages of dynamical coupling by implementing a novel adiabatic controlled-z gate, with a speed approaching that of single-qubit gates. Integrating coherence and scalable control, the introduced qubit architecture provides a promising path towards large-scale quantum computation and simulation.

Vectorization for Molecular Dynamics on Intel Xeon Phi Corpocessors

NASA Astrophysics Data System (ADS)

Yi, Hongsuk

2014-03-01

Many modern processors are capable of exploiting data-level parallelism through the use of single instruction multiple data (SIMD) execution. The new Intel Xeon Phi coprocessor supports 512 bit vector registers for the high performance computing. In this paper, we have developed a hierarchical parallelization scheme for accelerated molecular dynamics simulations with the Terfoff potentials for covalent bond solid crystals on Intel Xeon Phi coprocessor systems. The scheme exploits multi-level parallelism computing. We combine thread-level parallelism using a tightly coupled thread-level and task-level parallelism with 512-bit vector register. The simulation results show that the parallel performance of SIMD implementations on Xeon Phi is apparently superior to their x86 CPU architecture.

MODELING FUNCTIONALLY GRADED INTERPHASE REGIONS IN CARBON NANOTUBE REINFORCED COMPOSITES

NASA Technical Reports Server (NTRS)

Seidel, G. D.; Lagoudas, D. C.; Frankland, S. J. V.; Gates, T. S.

2006-01-01

A combination of micromechanics methods and molecular dynamics simulations are used to obtain the effective properties of the carbon nanotube reinforced composites with functionally graded interphase regions. The multilayer composite cylinders method accounts for the effects of non-perfect load transfer in carbon nanotube reinforced polymer matrix composites using a piecewise functionally graded interphase. The functional form of the properties in the interphase region, as well as the interphase thickness, is derived from molecular dynamics simulations of carbon nanotubes in a polymer matrix. Results indicate that the functional form of the interphase can have a significant effect on all the effective elastic constants except for the effective axial modulus for which no noticeable effects are evident.

Computational Fluid Dynamics Study of Swimmer's Hand Velocity, Orientation, and Shape: Contributions to Hydrodynamics

PubMed Central

Bilinauskaite, Milda; Mantha, Vishveshwar Rajendra; Rouboa, Abel Ilah; Ziliukas, Pranas; Silva, Antonio Jose

2013-01-01

The aim of this paper is to determine the hydrodynamic characteristics of swimmer's scanned hand models for various combinations of both the angle of attack and the sweepback angle and shape and velocity of swimmer's hand, simulating separate underwater arm stroke phases of freestyle (front crawl) swimming. Four realistic 3D models of swimmer's hand corresponding to different combinations of separated/closed fingers positions were used to simulate different underwater front crawl phases. The fluid flow was simulated using FLUENT (ANSYS, PA, USA). Drag force and drag coefficient were calculated using (computational fluid dynamics) CFD in steady state. Results showed that the drag force and coefficient varied at the different flow velocities on all shapes of the hand and variation was observed for different hand positions corresponding to different stroke phases. The models of the hand with thumb adducted and abducted generated the highest drag forces and drag coefficients. The current study suggests that the realistic variation of both the orientation angles influenced higher values of drag, lift, and resultant coefficients and forces. To augment resultant force, which affects swimmer's propulsion, the swimmer should concentrate in effectively optimising achievable hand areas during crucial propulsive phases. PMID:23691493

Achieving Remission in Gulf War Illness: A Simulation-Based Approach to Treatment Design.

PubMed

Craddock, Travis J A; Del Rosario, Ryan R; Rice, Mark; Zysman, Joel P; Fletcher, Mary Ann; Klimas, Nancy G; Broderick, Gordon

2015-01-01

Gulf War Illness (GWI) is a chronic multi-symptom disorder affecting up to one-third of the 700,000 returning veterans of the 1991 Persian Gulf War and for which there is no known cure. GWI symptoms span several of the body's principal regulatory systems and include debilitating fatigue, severe musculoskeletal pain, cognitive and neurological problems. Using computational models, our group reported previously that GWI might be perpetuated at least in part by natural homeostatic regulation of the neuroendocrine-immune network. In this work, we attempt to harness these regulatory dynamics to identify treatment courses that might produce lasting remission. Towards this we apply a combinatorial optimization scheme to the Monte Carlo simulation of a discrete ternary logic model that represents combined hypothalamic-pituitary-adrenal (HPA), gonadal (HPG), and immune system regulation in males. In this work we found that no single intervention target allowed a robust return to normal homeostatic control. All combined interventions leading to a predicted remission involved an initial inhibition of Th1 inflammatory cytokines (Th1Cyt) followed by a subsequent inhibition of glucocorticoid receptor function (GR). These first two intervention events alone ended in stable and lasting return to the normal regulatory control in 40% of the simulated cases. Applying a second cycle of this combined treatment improved this predicted remission rate to 2 out of 3 simulated subjects (63%). These results suggest that in a complex illness such as GWI, a multi-tiered intervention strategy that formally accounts for regulatory dynamics may be required to reset neuroendocrine-immune homeostasis and support extended remission.

Combination and selection of traffic safety expert judgments for the prevention of driving risks.

PubMed

Cabello, Enrique; Conde, Cristina; de Diego, Isaac Martín; Moguerza, Javier M; Redchuk, Andrés

2012-11-02

In this paper, we describe a new framework to combine experts’ judgments for the prevention of driving risks in a cabin truck. In addition, the methodology shows how to choose among the experts the one whose predictions fit best the environmental conditions. The methodology is applied over data sets obtained from a high immersive cabin truck simulator in natural driving conditions. A nonparametric model, based in Nearest Neighbors combined with Restricted Least Squared methods is developed. Three experts were asked to evaluate the driving risk using a Visual Analog Scale (VAS), in order to measure the driving risk in a truck simulator where the vehicle dynamics factors were stored. Numerical results show that the methodology is suitable for embedding in real time systems.

Investigation of the Dayton IR 75 sign truss failure of 9/11/06.

DOT National Transportation Integrated Search

2007-03-01

Based upon a combination of in-situ field monitoring of traffic-induced bridge : vibrations at the location of the failed sign support truss, finite element simulation of the : expected dynamic response of the original truss in such an environment, t...

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

DOE PAGES

Song, Lingshuang; Yang, Lin; Meng, Jie; ...

2016-12-29

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1. Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostlymore » in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.« less

Revealing spatially heterogeneous relaxation in a model nanocomposite.

PubMed

Cheng, Shiwang; Mirigian, Stephen; Carrillo, Jan-Michael Y; Bocharova, Vera; Sumpter, Bobby G; Schweizer, Kenneth S; Sokolov, Alexei P

2015-11-21

The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility gradient shows no "glassy" layer, but the α-relaxation time near the nanoparticle grows with cooling faster than the α-relaxation time in the bulk and is ∼20 times longer at low temperatures. The interfacial layer thickness increases from ∼1.8 nm at higher temperatures to ∼3.5 nm upon cooling to near bulk Tg. A real space microscopic description of the mobility gradient is constructed by synergistically combining high temperature atomistic simulation with theory. Our analysis suggests that the interfacial slowing down arises mainly due to an increase of the local cage scale barrier for activated hopping induced by enhanced packing and densification near the nanoparticle surface. The theory is employed to predict how local surface densification can be manipulated to control layer dynamics and shear rigidity over a wide temperature range.

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental–Computational Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Lingshuang; Yang, Lin; Meng, Jie

Here, we present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure inter-leucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å -1. Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0$-$1.5 Å -1). This experimental-computational consistence enables a first glimpse of the leucineleucine interacting landscape, where two leucine molecules are aligned mostlymore » in a parallel fashion, as opposed to anti-parallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables a quantitative characterization on effective inter-molecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.« less

Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches.

PubMed

Jiang, Hanlun; Zhu, Lizhe; Héliou, Amélie; Gao, Xin; Bernauer, Julie; Huang, Xuhui

2017-01-01

MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling

NASA Astrophysics Data System (ADS)

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.

PubMed

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

Dynamics and Control of Flexible Space Vehicles

NASA Technical Reports Server (NTRS)

Likins, P. W.

1970-01-01

The purpose of this report is twofold: (1) to survey the established analytic procedures for the simulation of controlled flexible space vehicles, and (2) to develop in detail methods that employ a combination of discrete and distributed ("modal") coordinates, i.e., the hybrid-coordinate methods. Analytic procedures are described in three categories: (1) discrete-coordinate methods, (2) hybrid-coordinate methods, and (3) vehicle normal-coordinate methods. Each of these approaches is described and analyzed for its advantages and disadvantages, and each is found to have an area of applicability. The hybrid-coordinate method combines the efficiency of the vehicle normal-coordinate method with the versatility of the discrete-coordinate method, and appears to have the widest range of practical application. The results in this report have practical utility in two areas: (1) complex digital computer simulation of flexible space vehicles of arbitrary configuration subject to realistic control laws, and (2) preliminary control system design based on transfer functions for linearized models of dynamics and control laws.

Revealing spatially heterogeneous relaxation in a model nanocomposite

DOE PAGES

Cheng, Shiwang; Mirigian, Stephen; Carrillo, Jan-Michael Y.; ...

2015-11-18

The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility gradient shows no glassy layer, but the -relaxation time near the nanoparticle grows with cooling faster than the -relaxation time in the bulk and is ~20 times longer at low temperatures. The interfacial layer thickness increases from ~1.8 nm at higher temperatures to ~3.5 nm upon cooling to near bulk T g. A real space microscopic description of the mobility gradient is constructed by synergistically combining high temperature atomistic simulation with theory.more » Our analysis suggests that the interfacial slowing down arises mainly due to an increase of the local cage scale barrier for activated hopping induced by enhanced packing and densification near the nanoparticle surface. As a result, the theory is employed to predict how local surface densification can be manipulated to control layer dynamics and shear rigidity over a wide temperature range.« less

Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

PubMed

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

Exploring the Dynamics of Cell Processes through Simulations of Fluorescence Microscopy Experiments

PubMed Central

Angiolini, Juan; Plachta, Nicolas; Mocskos, Esteban; Levi, Valeria

2015-01-01

Fluorescence correlation spectroscopy (FCS) methods are powerful tools for unveiling the dynamical organization of cells. For simple cases, such as molecules passively moving in a homogeneous media, FCS analysis yields analytical functions that can be fitted to the experimental data to recover the phenomenological rate parameters. Unfortunately, many dynamical processes in cells do not follow these simple models, and in many instances it is not possible to obtain an analytical function through a theoretical analysis of a more complex model. In such cases, experimental analysis can be combined with Monte Carlo simulations to aid in interpretation of the data. In response to this need, we developed a method called FERNET (Fluorescence Emission Recipes and Numerical routines Toolkit) based on Monte Carlo simulations and the MCell-Blender platform, which was designed to treat the reaction-diffusion problem under realistic scenarios. This method enables us to set complex geometries of the simulation space, distribute molecules among different compartments, and define interspecies reactions with selected kinetic constants, diffusion coefficients, and species brightness. We apply this method to simulate single- and multiple-point FCS, photon-counting histogram analysis, raster image correlation spectroscopy, and two-color fluorescence cross-correlation spectroscopy. We believe that this new program could be very useful for predicting and understanding the output of fluorescence microscopy experiments. PMID:26039162

Transition Pathway and Its Free-Energy Profile: A Protocol for Protein Folding Simulations

PubMed Central

Lee, In-Ho; Kim, Seung-Yeon; Lee, Jooyoung

2013-01-01

We propose a protocol that provides a systematic definition of reaction coordinate and related free-energy profile as the function of temperature for the protein-folding simulation. First, using action-derived molecular dynamics (ADMD), we investigate the dynamic folding pathway model of a protein between a fixed extended conformation and a compact conformation. We choose the pathway model to be the reaction coordinate, and the folding and unfolding processes are characterized by the ADMD step index, in contrast to the common a priori reaction coordinate as used in conventional studies. Second, we calculate free-energy profile as the function of temperature, by employing the replica-exchange molecular dynamics (REMD) method. The current method provides efficient exploration of conformational space and proper characterization of protein folding/unfolding dynamics from/to an arbitrary extended conformation. We demonstrate that combination of the two simulation methods, ADMD and REMD, provides understanding on molecular conformational changes in proteins. The protocol is tested on a small protein, penta-peptide of met-enkephalin. For the neuropeptide met-enkephalin system, folded, extended, and intermediate sates are well-defined through the free-energy profile over the reaction coordinate. Results are consistent with those in the literature. PMID:23917881

Large-Scale Dynamics of the Magnetospheric Boundary: Comparisons between Global MHD Simulation Results and ISTP Observations

NASA Technical Reports Server (NTRS)

Berchem, J.; Raeder, J.; Ashour-Abdalla, M.; Frank, L. A.; Paterson, W. R.; Ackerson, K. L.; Kokubun, S.; Yamamoto, T.; Lepping, R. P.

1998-01-01

Understanding the large-scale dynamics of the magnetospheric boundary is an important step towards achieving the ISTP mission's broad objective of assessing the global transport of plasma and energy through the geospace environment. Our approach is based on three-dimensional global magnetohydrodynamic (MHD) simulations of the solar wind-magnetosphere- ionosphere system, and consists of using interplanetary magnetic field (IMF) and plasma parameters measured by solar wind monitors upstream of the bow shock as input to the simulations for predicting the large-scale dynamics of the magnetospheric boundary. The validity of these predictions is tested by comparing local data streams with time series measured by downstream spacecraft crossing the magnetospheric boundary. In this paper, we review results from several case studies which confirm that our MHD model reproduces very well the large-scale motion of the magnetospheric boundary. The first case illustrates the complexity of the magnetic field topology that can occur at the dayside magnetospheric boundary for periods of northward IMF with strong Bx and By components. The second comparison reviewed combines dynamic and topological aspects in an investigation of the evolution of the distant tail at 200 R(sub E) from the Earth.

An ice sheet model validation framework for the Greenland ice sheet

NASA Astrophysics Data System (ADS)

Price, Stephen F.; Hoffman, Matthew J.; Bonin, Jennifer A.; Howat, Ian M.; Neumann, Thomas; Saba, Jack; Tezaur, Irina; Guerber, Jeffrey; Chambers, Don P.; Evans, Katherine J.; Kennedy, Joseph H.; Lenaerts, Jan; Lipscomb, William H.; Perego, Mauro; Salinger, Andrew G.; Tuminaro, Raymond S.; van den Broeke, Michiel R.; Nowicki, Sophie M. J.

2017-01-01

We propose a new ice sheet model validation framework - the Cryospheric Model Comparison Tool (CmCt) - that takes advantage of ice sheet altimetry and gravimetry observations collected over the past several decades and is applied here to modeling of the Greenland ice sheet. We use realistic simulations performed with the Community Ice Sheet Model (CISM) along with two idealized, non-dynamic models to demonstrate the framework and its use. Dynamic simulations with CISM are forced from 1991 to 2013, using combinations of reanalysis-based surface mass balance and observations of outlet glacier flux change. We propose and demonstrate qualitative and quantitative metrics for use in evaluating the different model simulations against the observations. We find that the altimetry observations used here are largely ambiguous in terms of their ability to distinguish one simulation from another. Based on basin-scale and whole-ice-sheet-scale metrics, we find that simulations using both idealized conceptual models and dynamic, numerical models provide an equally reasonable representation of the ice sheet surface (mean elevation differences of < 1 m). This is likely due to their short period of record, biases inherent to digital elevation models used for model initial conditions, and biases resulting from firn dynamics, which are not explicitly accounted for in the models or observations. On the other hand, we find that the gravimetry observations used here are able to unambiguously distinguish between simulations of varying complexity, and along with the CmCt, can provide a quantitative score for assessing a particular model and/or simulation. The new framework demonstrates that our proposed metrics can distinguish relatively better from relatively worse simulations and that dynamic ice sheet models, when appropriately initialized and forced with the right boundary conditions, demonstrate a predictive skill with respect to observed dynamic changes that have occurred on Greenland over the past few decades. An extensible design will allow for continued use of the CmCt as future altimetry, gravimetry, and other remotely sensed data become available for use in ice sheet model validation.

An ice sheet model validation framework for the Greenland ice sheet

PubMed Central

Price, Stephen F.; Hoffman, Matthew J.; Bonin, Jennifer A.; Howat, Ian M.; Neumann, Thomas; Saba, Jack; Tezaur, Irina; Guerber, Jeffrey; Chambers, Don P.; Evans, Katherine J.; Kennedy, Joseph H.; Lenaerts, Jan; Lipscomb, William H.; Perego, Mauro; Salinger, Andrew G.; Tuminaro, Raymond S.; van den Broeke, Michiel R.; Nowicki, Sophie M. J.

2018-01-01

We propose a new ice sheet model validation framework – the Cryospheric Model Comparison Tool (CmCt) – that takes advantage of ice sheet altimetry and gravimetry observations collected over the past several decades and is applied here to modeling of the Greenland ice sheet. We use realistic simulations performed with the Community Ice Sheet Model (CISM) along with two idealized, non-dynamic models to demonstrate the framework and its use. Dynamic simulations with CISM are forced from 1991 to 2013 using combinations of reanalysis-based surface mass balance and observations of outlet glacier flux change. We propose and demonstrate qualitative and quantitative metrics for use in evaluating the different model simulations against the observations. We find that the altimetry observations used here are largely ambiguous in terms of their ability to distinguish one simulation from another. Based on basin- and whole-ice-sheet scale metrics, we find that simulations using both idealized conceptual models and dynamic, numerical models provide an equally reasonable representation of the ice sheet surface (mean elevation differences of <1 m). This is likely due to their short period of record, biases inherent to digital elevation models used for model initial conditions, and biases resulting from firn dynamics, which are not explicitly accounted for in the models or observations. On the other hand, we find that the gravimetry observations used here are able to unambiguously distinguish between simulations of varying complexity, and along with the CmCt, can provide a quantitative score for assessing a particular model and/or simulation. The new framework demonstrates that our proposed metrics can distinguish relatively better from relatively worse simulations and that dynamic ice sheet models, when appropriately initialized and forced with the right boundary conditions, demonstrate predictive skill with respect to observed dynamic changes occurring on Greenland over the past few decades. An extensible design will allow for continued use of the CmCt as future altimetry, gravimetry, and other remotely sensed data become available for use in ice sheet model validation. PMID:29697704

An Ice Sheet Model Validation Framework for the Greenland Ice Sheet

NASA Technical Reports Server (NTRS)

Price, Stephen F.; Hoffman, Matthew J.; Bonin, Jennifer A.; Howat, Ian M.; Neumann, Thomas A.; Saba, Jack; Tezaur, Irina; Guerber, Jeffrey R.; Chambers, Don P.; Evans, Katherine J.;

Molecular Dynamics Simulations Provide Atomistic Insight into Hydrogen Exchange Mass Spectrometry Experiments.

PubMed

Petruk, Ariel A; Defelipe, Lucas A; Rodríguez Limardo, Ramiro G; Bucci, Hernán; Marti, Marcelo A; Turjanski, Adrian G

2013-01-08

It is now clear that proteins are flexible entities that in solution switch between conformations to achieve their function. Hydrogen/Deuterium Exchange Mass Spectrometry (HX/MS) is an invaluable tool to understand dynamic changes in proteins modulated by cofactor binding, post-transductional modifications, or protein-protein interactions. ERK2MAPK, a protein involved in highly conserved signal transduction pathways of paramount importance for normal cellular function, has been extensively studied by HX/MS. Experiments of the ERK2MAPK in the inactive and active states (in the presence or absence of bound ATP) have provided valuable information on the plasticity of the MAPK domain. However, interpretation of the HX/MS data is difficult, and changes are mostly explained in relation to available X-ray structures, precluding a complete atomic picture of protein dynamics. In the present work, we have used all atom Molecular Dynamics simulations (MD) to provide a theoretical framework for the interpretation of HX/MS data. Our results show that detailed analysis of protein-solvent interaction along the MD simulations allows (i) prediction of the number of protons exchanged for each peptide in the HX/MS experiments, (ii) rationalization of the experimentally observed changes in exchange rates in different protein conditions at the residue level, and (iii) that at least for ERK2MAPK, most of the functionally observed differences in protein dynamics are related to what can be considered the native state conformational ensemble. In summary, the combination of HX/MS experiments with all atom MD simulations emerges as a powerful approach to study protein native state dynamics with atomic resolution.

Dynamic characteristic of electromechanical coupling effects in motor-gear system

NASA Astrophysics Data System (ADS)

Bai, Wenyu; Qin, Datong; Wang, Yawen; Lim, Teik C.

2018-06-01

Dynamic characteristics of an electromechanical model which combines a nonlinear permeance network model (PNM) of a squirrel-cage induction motor and a coupled lateral-torsional dynamic model of a planetary geared rotor system is analyzed in this study. The simulations reveal the effects of internal excitations or parameters like machine slotting, magnetic saturation, time-varying mesh stiffness and shaft stiffness on the system dynamics. The responses of the electromechanical system with PNM motor model are compared with those responses of the system with dynamic motor model. The electromechanical coupling due to the interactions between the motor and gear system are studied. Furthermore, the frequency analysis of the electromechanical system dynamic characteristics predicts an efficient way to detect work condition of unsymmetrical voltage sag.

The impact of dynamic data assimilation on the numerical simulations of the QE II cyclone and an analysis of the jet streak influencing the precyclogenetic environment

NASA Technical Reports Server (NTRS)

Manobianco, John; Uccellini, Louis W.; Brill, Keith F.; Kuo, Ying-Hwa

1992-01-01

A mesoscale numerical model is combined with a dynamic data assimilation via Newtonian relaxation, or 'nudging', to provide initial conditions for subsequent simulations of the QE II cyclone. Both the nudging technique and the inclusion of supplementary data are shown to have a large positive impact on the simulation of the QE II cyclone during the initial phase of rapid cyclone development. Within the initial development period (from 1200 to 1800 UTC 9 September 1978), the dynamic assimilation of operational and bogus data yields a coherent two-layer divergence pattern that is not well defined in the model run using only the operational data and static initialization. Diagnostic analysis based on the simulations show that the initial development of the QE II storm between 0000 UTC 9 September and 0000 UTC 10 September was embedded within an indirect circulation of an intense 300-hPa jet streak, was related to baroclinic processes extending throughout a deep portion of the troposphere, and was associated with a classic two-layer mass-divergence profile expected for an extratropical cyclone.

CALM: Complex Adaptive System (CAS)-Based Decision Support for Enabling Organizational Change

NASA Astrophysics Data System (ADS)

Adler, Richard M.; Koehn, David J.

Guiding organizations through transformational changes such as restructuring or adopting new technologies is a daunting task. Such changes generate workforce uncertainty, fear, and resistance, reducing morale, focus and performance. Conventional project management techniques fail to mitigate these disruptive effects, because social and individual changes are non-mechanistic, organic phenomena. CALM (for Change, Adaptation, Learning Model) is an innovative decision support system for enabling change based on CAS principles. CALM provides a low risk method for validating and refining change strategies that combines scenario planning techniques with "what-if" behavioral simulation. In essence, CALM "test drives" change strategies before rolling them out, allowing organizations to practice and learn from virtual rather than actual mistakes. This paper describes the CALM modeling methodology, including our metrics for measuring organizational readiness to respond to change and other major CALM scenario elements: prospective change strategies; alternate futures; and key situational dynamics. We then describe CALM's simulation engine for projecting scenario outcomes and its associated analytics. CALM's simulator unifies diverse behavioral simulation paradigms including: adaptive agents; system dynamics; Monte Carlo; event- and process-based techniques. CALM's embodiment of CAS dynamics helps organizations reduce risk and improve confidence and consistency in critical strategies for enabling transformations.

Adaptive critics for dynamic optimization.

PubMed

Kulkarni, Raghavendra V; Venayagamoorthy, Ganesh Kumar

2010-06-01

A novel action-dependent adaptive critic design (ACD) is developed for dynamic optimization. The proposed combination of a particle swarm optimization-based actor and a neural network critic is demonstrated through dynamic sleep scheduling of wireless sensor motes for wildlife monitoring. The objective of the sleep scheduler is to dynamically adapt the sleep duration to node's battery capacity and movement pattern of animals in its environment in order to obtain snapshots of the animal on its trajectory uniformly. Simulation results show that the sleep time of the node determined by the actor critic yields superior quality of sensory data acquisition and enhanced node longevity. Copyright 2010 Elsevier Ltd. All rights reserved.

Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.

PubMed

Roe, Daniel R; Bergonzo, Christina; Cheatham, Thomas E

2014-04-03

Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency.

Next generation extended Lagrangian first principles molecular dynamics

NASA Astrophysics Data System (ADS)

Niklasson, Anders M. N.

2017-08-01

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

Next generation extended Lagrangian first principles molecular dynamics.

PubMed

Niklasson, Anders M N

2017-08-07

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

A dynamic structural model of expanded RNA CAG repeats: A refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations

PubMed Central

Yildirim, Ilyas; Park, Hajeung; Disney, Matthew D.; Schatz, George C.

2013-01-01

One class of functionally important RNA is repeating transcripts that cause disease through various mechanisms. For example, expanded r(CAG) repeats can cause Huntington’s and other disease through translation of toxic proteins. Herein, crystal structure of r[5ʹUUGGGC(CAG)3GUCC]2, a model of CAG expanded transcripts, refined to 1.65 Å resolution is disclosed that show both anti-anti and syn-anti orientations for 1×1 nucleotide AA internal loops. Molecular dynamics (MD) simulations using Amber force field in explicit solvent were run for over 500 ns on model systems r(5ʹGCGCAGCGC)2 (MS1) and r(5ʹCCGCAGCGG)2 (MS2). In these MD simulations, both anti-anti and syn-anti AA base pairs appear to be stable. While anti-anti AA base pairs were dynamic and sampled multiple anti-anti conformations, no syn-anti↔anti-anti transformations were observed. Umbrella sampling simulations were run on MS2, and a 2D free energy surface was created to extract transformation pathways. In addition, over 800 ns explicit solvent MD simulation was run on r[5ʹGGGC(CAG)3GUCC]2, which closely represents the refined crystal structure. One of the terminal AA base pairs (syn-anti conformation), transformed to anti-anti conformation. The pathway followed in this transformation was the one predicted by umbrella sampling simulations. Further analysis showed a binding pocket near AA base pairs in syn-anti conformations. Computational results combined with the refined crystal structure show that global minimum conformation of 1×1 nucleotide AA internal loops in r(CAG) repeats is anti-anti but can adopt syn-anti depending on the environment. These results are important to understand RNA dynamic-function relationships and develop small molecules that target RNA dynamic ensembles. PMID:23441937

Three-dimensional plant architecture and sunlit-shaded patterns: a stochastic model of light dynamics in canopies.

PubMed

Retkute, Renata; Townsend, Alexandra J; Murchie, Erik H; Jensen, Oliver E; Preston, Simon P

2018-05-25

Diurnal changes in solar position and intensity combined with the structural complexity of plant architecture result in highly variable and dynamic light patterns within the plant canopy. This affects productivity through the complex ways that photosynthesis responds to changes in light intensity. Current methods to characterize light dynamics, such as ray-tracing, are able to produce data with excellent spatio-temporal resolution but are computationally intensive and the resulting data are complex and high-dimensional. This necessitates development of more economical models for summarizing the data and for simulating realistic light patterns over the course of a day. High-resolution reconstructions of field-grown plants are assembled in various configurations to form canopies, and a forward ray-tracing algorithm is applied to the canopies to compute light dynamics at high (1 min) temporal resolution. From the ray-tracer output, the sunlit or shaded state for each patch on the plants is determined, and these data are used to develop a novel stochastic model for the sunlit-shaded patterns. The model is designed to be straightforward to fit to data using maximum likelihood estimation, and fast to simulate from. For a wide range of contrasting 3-D canopies, the stochastic model is able to summarize, and replicate in simulations, key features of the light dynamics. When light patterns simulated from the stochastic model are used as input to a model of photoinhibition, the predicted reduction in carbon gain is similar to that from calculations based on the (extremely costly) ray-tracer data. The model provides a way to summarize highly complex data in a small number of parameters, and a cost-effective way to simulate realistic light patterns. Simulations from the model will be particularly useful for feeding into larger-scale photosynthesis models for calculating how light dynamics affects the photosynthetic productivity of canopies.

Simulating large-scale pedestrian movement using CA and event driven model: Methodology and case study

NASA Astrophysics Data System (ADS)

Li, Jun; Fu, Siyao; He, Haibo; Jia, Hongfei; Li, Yanzhong; Guo, Yi

2015-11-01

Large-scale regional evacuation is an important part of national security emergency response plan. Large commercial shopping area, as the typical service system, its emergency evacuation is one of the hot research topics. A systematic methodology based on Cellular Automata with the Dynamic Floor Field and event driven model has been proposed, and the methodology has been examined within context of a case study involving the evacuation within a commercial shopping mall. Pedestrians walking is based on Cellular Automata and event driven model. In this paper, the event driven model is adopted to simulate the pedestrian movement patterns, the simulation process is divided into normal situation and emergency evacuation. The model is composed of four layers: environment layer, customer layer, clerk layer and trajectory layer. For the simulation of movement route of pedestrians, the model takes into account purchase intention of customers and density of pedestrians. Based on evacuation model of Cellular Automata with Dynamic Floor Field and event driven model, we can reflect behavior characteristics of customers and clerks at the situations of normal and emergency evacuation. The distribution of individual evacuation time as a function of initial positions and the dynamics of the evacuation process is studied. Our results indicate that the evacuation model using the combination of Cellular Automata with Dynamic Floor Field and event driven scheduling can be used to simulate the evacuation of pedestrian flows in indoor areas with complicated surroundings and to investigate the layout of shopping mall.

Application of a computationally efficient method to approximate gap model results with a probabilistic approach

NASA Astrophysics Data System (ADS)

Scherstjanoi, M.; Kaplan, J. O.; Lischke, H.

2014-07-01

To be able to simulate climate change effects on forest dynamics over the whole of Switzerland, we adapted the second-generation DGVM (dynamic global vegetation model) LPJ-GUESS (Lund-Potsdam-Jena General Ecosystem Simulator) to the Alpine environment. We modified model functions, tuned model parameters, and implemented new tree species to represent the potential natural vegetation of Alpine landscapes. Furthermore, we increased the computational efficiency of the model to enable area-covering simulations in a fine resolution (1 km) sufficient for the complex topography of the Alps, which resulted in more than 32 000 simulation grid cells. To this aim, we applied the recently developed method GAPPARD (approximating GAP model results with a Probabilistic Approach to account for stand Replacing Disturbances) (Scherstjanoi et al., 2013) to LPJ-GUESS. GAPPARD derives mean output values from a combination of simulation runs without disturbances and a patch age distribution defined by the disturbance frequency. With this computationally efficient method, which increased the model's speed by approximately the factor 8, we were able to faster detect the shortcomings of LPJ-GUESS functions and parameters. We used the adapted LPJ-GUESS together with GAPPARD to assess the influence of one climate change scenario on dynamics of tree species composition and biomass throughout the 21st century in Switzerland. To allow for comparison with the original model, we additionally simulated forest dynamics along a north-south transect through Switzerland. The results from this transect confirmed the high value of the GAPPARD method despite some limitations towards extreme climatic events. It allowed for the first time to obtain area-wide, detailed high-resolution LPJ-GUESS simulation results for a large part of the Alpine region.

Virtual reality in neurosurgical education: part-task ventriculostomy simulation with dynamic visual and haptic feedback.

PubMed

Lemole, G Michael; Banerjee, P Pat; Luciano, Cristian; Neckrysh, Sergey; Charbel, Fady T

2007-07-01

Mastery of the neurosurgical skill set involves many hours of supervised intraoperative training. Convergence of political, economic, and social forces has limited neurosurgical resident operative exposure. There is need to develop realistic neurosurgical simulations that reproduce the operative experience, unrestricted by time and patient safety constraints. Computer-based, virtual reality platforms offer just such a possibility. The combination of virtual reality with dynamic, three-dimensional stereoscopic visualization, and haptic feedback technologies makes realistic procedural simulation possible. Most neurosurgical procedures can be conceptualized and segmented into critical task components, which can be simulated independently or in conjunction with other modules to recreate the experience of a complex neurosurgical procedure. We use the ImmersiveTouch (ImmersiveTouch, Inc., Chicago, IL) virtual reality platform, developed at the University of Illinois at Chicago, to simulate the task of ventriculostomy catheter placement as a proof-of-concept. Computed tomographic data are used to create a virtual anatomic volume. Haptic feedback offers simulated resistance and relaxation with passage of a virtual three-dimensional ventriculostomy catheter through the brain parenchyma into the ventricle. A dynamic three-dimensional graphical interface renders changing visual perspective as the user's head moves. The simulation platform was found to have realistic visual, tactile, and handling characteristics, as assessed by neurosurgical faculty, residents, and medical students. We have developed a realistic, haptics-based virtual reality simulator for neurosurgical education. Our first module recreates a critical component of the ventriculostomy placement task. This approach to task simulation can be assembled in a modular manner to reproduce entire neurosurgical procedures.

Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube.

PubMed

Duster, Adam W; Lin, Hai

2017-09-14

Recently, a collective variable "proton indicator" was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore. This is consistent with an earlier study that employed a multistate empirical valence bond potential and a different representation (center of excess charge) of the proton. We attribute this water recruitment to the delocalized nature of the solvated proton, which prefers to be in high-dielectric bulk solvent. While water recruitment into the pore is considered an artifact in the present simulations (because of the artificially imposed restraint on the proton), if the proton were naturally restrained, it could assist in building water wires prior to proton transfer through the pore. The potential of mean force for a proton translocation through the water-filled pore was computed by umbrella sampling, where the bias potentials were applied to the proton indicator. The free energy curve and barrier heights agree reasonably with those in the literature. The results suggest that the proton indicator can be used as a reaction coordinate in simulations of proton transport in confined environments.

Optimal control of energy extraction in LES of large wind farms

NASA Astrophysics Data System (ADS)

Meyers, Johan; Goit, Jay; Munters, Wim

2014-11-01

We investigate the use of optimal control combined with Large-Eddy Simulations (LES) of wind-farm boundary layer interaction for the increase of total energy extraction in very large ``infinite'' wind farms and in finite farms. We consider the individual wind turbines as flow actuators, whose energy extraction can be dynamically regulated in time so as to optimally influence the turbulent flow field, maximizing the wind farm power. For the simulation of wind-farm boundary layers we use large-eddy simulations in combination with an actuator-disk representation of wind turbines. Simulations are performed in our in-house pseudo-spectral code SP-Wind. For the optimal control study, we consider the dynamic control of turbine-thrust coefficients in the actuator-disk model. They represent the effect of turbine blades that can actively pitch in time, changing the lift- and drag coefficients of the turbine blades. In a first infinite wind-farm case, we find that farm power is increases by approximately 16% over one hour of operation. This comes at the cost of a deceleration of the outer layer of the boundary layer. A detailed analysis of energy balances is presented, and a comparison is made between infinite and finite farm cases, for which boundary layer entrainment plays an import role. The authors acknowledge support from the European Research Council (FP7-Ideas, Grant No. 306471). Simulations were performed on the computing infrastructure of the VSC Flemish Supercomputer Center, funded by the Hercules Foundation and the Flemish Govern.

Molecular-dynamics simulation of mutual diffusion in nonideal liquid mixtures

NASA Astrophysics Data System (ADS)

Rowley, R. L.; Stoker, J. M.; Giles, N. F.

1991-05-01

The mutual-diffusion coefficients, D 12, of n-hexane, n-heptane, and n-octane in chloroform were modeled using equilibrium molecular-dynamics (MD) simulations of simple Lennard-Jones (LJ) fluids. Pure-component LJ parameters were obtained by comparison of simulations to experimental self-diffusion coefficients. While values of “effective” LJ parameters are not expected to simulate accurately diverse thermophysical properties over a wide range of conditions, it was recently shown that effective parameters obtained from pure self-diffusion coefficients can accurately model mutual diffusion in ideal, liquid mixtures. In this work, similar simulations are used to model diffusion in nonideal mixtures. The same combining rules used in the previous study for the cross-interaction parameters were found to be adequate to represent the composition dependence of D 12. The effect of alkane chain length on D 12 is also correctly predicted by the simulations. A commonly used assumption in empirical correlations of D 12, that its kinetic portion is a simple, compositional average of the intradiffusion coefficients, is inconsistent with the simulation results. In fact, the value of the kinetic portion of D 12 was often outside the range of values bracketed by the two intradiffusion coefficients for the nonideal system modeled here.

Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models

NASA Astrophysics Data System (ADS)

Dodani, Sheel C.; Kiss, Gert; Cahn, Jackson K. B.; Su, Ye; Pande, Vijay S.; Arnold, Frances H.

2016-05-01

The dynamic motions of protein structural elements, particularly flexible loops, are intimately linked with diverse aspects of enzyme catalysis. Engineering of these loop regions can alter protein stability, substrate binding and even dramatically impact enzyme function. When these flexible regions are unresolvable structurally, computational reconstruction in combination with large-scale molecular dynamics simulations can be used to guide the engineering strategy. Here we present a collaborative approach that consists of both experiment and computation and led to the discovery of a single mutation in the F/G loop of the nitrating cytochrome P450 TxtE that simultaneously controls loop dynamics and completely shifts the enzyme's regioselectivity from the C4 to the C5 position of L-tryptophan. Furthermore, we find that this loop mutation is naturally present in a subset of homologous nitrating P450s and confirm that these uncharacterized enzymes exclusively produce 5-nitro-L-tryptophan, a previously unknown biosynthetic intermediate.

FATE-HD: A spatially and temporally explicit integrated model for predicting vegetation structure and diversity at regional scale

PubMed Central

Isabelle, Boulangeat; Damien, Georges; Wilfried, Thuiller

2014-01-01

During the last decade, despite strenuous efforts to develop new models and compare different approaches, few conclusions have been drawn on their ability to provide robust biodiversity projections in an environmental change context. The recurring suggestions are that models should explicitly (i) include spatiotemporal dynamics; (ii) consider multiple species in interactions; and (iii) account for the processes shaping biodiversity distribution. This paper presents a biodiversity model (FATE-HD) that meets this challenge at regional scale by combining phenomenological and process-based approaches and using well-defined plant functional groups. FATE-HD has been tested and validated in a French National Park, demonstrating its ability to simulate vegetation dynamics, structure and diversity in response to disturbances and climate change. The analysis demonstrated the importance of considering biotic interactions, spatio-temporal dynamics, and disturbances in addition to abiotic drivers to simulate vegetation dynamics. The distribution of pioneer trees was particularly improved, as were all undergrowth functional groups. PMID:24214499

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach.

PubMed

Prior, Christopher; Oganesyan, Vasily S

2017-09-21

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatio-Temporal Process Simulation of Dam-Break Flood Based on SPH

NASA Astrophysics Data System (ADS)

Wang, H.; Ye, F.; Ouyang, S.; Li, Z.

2018-04-01

On the basis of introducing the SPH (Smooth Particle Hydrodynamics) simulation method, the key research problems were given solutions in this paper, which ere the spatial scale and temporal scale adapting to the GIS(Geographical Information System) application, the boundary condition equations combined with the underlying surface, and the kernel function and parameters applicable to dam-break flood simulation. In this regards, a calculation method of spatio-temporal process emulation with elaborate particles for dam-break flood was proposed. Moreover the spatio-temporal process was dynamic simulated by using GIS modelling and visualization. The results show that the method gets more information, objectiveness and real situations.

Molecular simulations of a CO2/CO mixture in MIL-127

NASA Astrophysics Data System (ADS)

Chokbunpiam, Tatiya; Fritzsche, Siegfried; Parasuk, Vudhichai; Caro, Jürgen; Assabumrungrat, Suttichai

2018-03-01

Adsorption and diffusion of an equimolar feed mixture of CO2 and CO in MIL-127 at three different temperatures and pressures up to 12 bar were investigated by molecular simulations. The adsorption was simulated using Gibbs-Ensemble Monte Carlo (GEMC). The structure of the adsorbed phase and the diffusion in the MIL were investigated using Molecular Dynamics (MD) simulations. The adsorption selectivity of MIL-127 for CO2 over CO at 233 K was about 15. When combining adsorption and diffusion selectivities, a membrane selectivity of about 12 is predicted. For higher temperatures, both adsorption and diffusion selectivity are found to be smaller.

Benefits Assessment of Algorithmically Combining Generic High Altitude Airspace Sectors

NASA Technical Reports Server (NTRS)

Bloem, Michael; Gupta, Pramod; Lai, Chok Fung; Kopardekar, Parimal

2009-01-01

In today's air traffic control operations, sectors that have traffic demand below capacity are combined so that fewer controller teams are required to manage air traffic. Controllers in current operations are certified to control a group of six to eight sectors, known as an area of specialization. Sector combinations are restricted to occur within areas of specialization. Since there are few sector combination possibilities in each area of specialization, human supervisors can effectively make sector combination decisions. In the future, automation and procedures will allow any appropriately trained controller to control any of a large set of generic sectors. The primary benefit of this will be increased controller staffing flexibility. Generic sectors will also allow more options for combining sectors, making sector combination decisions difficult for human supervisors. A sector-combining algorithm can assist supervisors as they make generic sector combination decisions. A heuristic algorithm for combining under-utilized air space sectors to conserve air traffic control resources has been described and analyzed. Analysis of the algorithm and comparisons with operational sector combinations indicate that this algorithm could more efficiently utilize air traffic control resources than current sector combinations. This paper investigates the benefits of using the sector-combining algorithm proposed in previous research to combine high altitude generic airspace sectors. Simulations are conducted in which all the high altitude sectors in a center are allowed to combine, as will be possible in generic high altitude airspace. Furthermore, the algorithm is adjusted to use a version of the simplified dynamic density (SDD) workload metric that has been modified to account for workload reductions due to automatic handoffs and Automatic Dependent Surveillance Broadcast (ADS-B). This modified metric is referred to here as future simplified dynamic density (FSDD). Finally, traffic demand sets with increased air traffic demand are used in the simulations to capture the expected growth in air traffic demand by the mid-term.

Chaotic Dynamics and Application of LCR Oscillators Sharing Common Nonlinearity

NASA Astrophysics Data System (ADS)

Jeevarekha, A.; Paul Asir, M.; Philominathan, P.

2016-06-01

This paper addresses the problem of sharing common nonlinearity among nonautonomous and autonomous oscillators. By choosing a suitable common nonlinear element with the driving point characteristics capable of bringing out chaotic motion in a combined system, we obtain identical chaotic states. The dynamics of the coupled system is explored through numerical and experimental studies. Employing the concept of common nonlinearity, a simple chaotic communication system is modeled and its performance is verified through Multisim simulation.

Understanding the effect of carbon status on stem diameter variations

PubMed Central

De Swaef, Tom; Driever, Steven M.; Van Meulebroek, Lieven; Vanhaecke, Lynn; Marcelis, Leo F. M.; Steppe, Kathy

2013-01-01

Background Carbon assimilation and leaf-to-fruit sugar transport are, along with plant water status, the driving mechanisms for fruit growth. An integrated comprehension of the plant water and carbon relationships is therefore essential to better understand water and dry matter accumulation. Variations in stem diameter result from an integrated response to plant water and carbon status and are as such a valuable source of information. Methods A mechanistic water flow and storage model was used to relate variations in stem diameter to phloem sugar loading and sugar concentration dynamics in tomato. The simulation results were compared with an independent model, simulating phloem sucrose loading at the leaf level based on photosynthesis and sugar metabolism kinetics and enabled a mechanistic interpretation of the ‘one common assimilate pool’ concept for tomato. Key Results Combining stem diameter variation measurements and mechanistic modelling allowed us to distinguish instantaneous dynamics in the plant water relations and gradual variations in plant carbon status. Additionally, the model combined with stem diameter measurements enabled prediction of dynamic variables which are difficult to measure in a continuous and non-destructive way, such as xylem water potential and phloem hydrostatic potential. Finally, dynamics in phloem sugar loading and sugar concentration were distilled from stem diameter variations. Conclusions Stem diameter variations, when used in mechanistic models, have great potential to continuously monitor and interpret plant water and carbon relations under natural growing conditions. PMID:23186836

Analysis of wind-resistant and stability for cable tower in cable-stayed bridge with four towers

NASA Astrophysics Data System (ADS)

Meng, Yangjun; Li, Can

2017-06-01

Wind speed time history simulation methods have been introduced first, especially the harmonic synthesis method introduced in detail. Second, taking Chishi bridge for example, choosing the particular sections, and combined with the design wind speed, three-component coefficient simulate analysis between -4°and 4°has been carry out with the Fluent software. The results show that drag coefficient reaches maximum when the attack Angle is 1°. According to measured wind speed samples,time history curves of wind speed at bridge deck and tower roof have been obtained,and wind-resistant time history analysis for No.5 tower has been carry out. Their results show that the dynamic coefficients are different with different calculation standard, especially transverse bending moment, pulsating crosswind load does not show a dynamic amplification effect.Under pulsating wind loads at bridge deck or tower roof, the maximum displacement at the top of the tower and the maximum stress at the bottom of the tower are within the allowable range. The transverse stiffness of tower is greater than that of the longitudinal stiffness, therefore wind-resistant analysis should give priority to the longitudinal direction. Dynamic coefficients are different with different standard, the maximum dynamic coefficient should be used for the pseudo-static analysis.Finally, the static stability of tower is analyzed with different load combinations, and the galloping stabilities of cable tower is proved.

A Study on Fast Gates for Large-Scale Quantum Simulation with Trapped Ions

PubMed Central

Taylor, Richard L.; Bentley, Christopher D. B.; Pedernales, Julen S.; Lamata, Lucas; Solano, Enrique; Carvalho, André R. R.; Hope, Joseph J.

2017-01-01

Large-scale digital quantum simulations require thousands of fundamental entangling gates to construct the simulated dynamics. Despite success in a variety of small-scale simulations, quantum information processing platforms have hitherto failed to demonstrate the combination of precise control and scalability required to systematically outmatch classical simulators. We analyse how fast gates could enable trapped-ion quantum processors to achieve the requisite scalability to outperform classical computers without error correction. We analyze the performance of a large-scale digital simulator, and find that fidelity of around 70% is realizable for π-pulse infidelities below 10−5 in traps subject to realistic rates of heating and dephasing. This scalability relies on fast gates: entangling gates faster than the trap period. PMID:28401945

A Study on Fast Gates for Large-Scale Quantum Simulation with Trapped Ions.

PubMed

Taylor, Richard L; Bentley, Christopher D B; Pedernales, Julen S; Lamata, Lucas; Solano, Enrique; Carvalho, André R R; Hope, Joseph J

2017-04-12

Large-scale digital quantum simulations require thousands of fundamental entangling gates to construct the simulated dynamics. Despite success in a variety of small-scale simulations, quantum information processing platforms have hitherto failed to demonstrate the combination of precise control and scalability required to systematically outmatch classical simulators. We analyse how fast gates could enable trapped-ion quantum processors to achieve the requisite scalability to outperform classical computers without error correction. We analyze the performance of a large-scale digital simulator, and find that fidelity of around 70% is realizable for π-pulse infidelities below 10 -5 in traps subject to realistic rates of heating and dephasing. This scalability relies on fast gates: entangling gates faster than the trap period.

Design parameters for tuning the type 1 Cu multicopper oxidase redox potential: insight from a combination of first principles and empirical molecular dynamics simulations.

PubMed

Hong, Gongyi; Ivnitski, Dmitri M; Johnson, Glenn R; Atanassov, Plamen; Pachter, Ruth

2011-04-06

The redox potentials and reorganization energies of the type 1 (T1) Cu site in four multicopper oxidases were calculated by combining first principles density functional theory (QM) and QM/MM molecular dynamics (MD) simulations. The model enzymes selected included the laccase from Trametes versicolor, the laccase-like enzyme isolated from Bacillus subtilis, CueO required for copper homeostasis in Escherichia coli, and the small laccase (SLAC) from Streptomyces coelicolor. The results demonstrated good agreement with experimental data and provided insight into the parameters that influence the T1 redox potential. Effects of the immediate T1 Cu site environment, including the His(N(δ))-Cys(S)-His(N(δ)) and the axial coordinating amino acid, as well as the proximate H(N)(backbone)-S(Cys) hydrogen bond, were discerned. Furthermore, effects of the protein backbone and side-chains, as well as of the aqueous solvent, were studied by QM/MM molecular dynamics (MD) simulations, providing an understanding of influences beyond the T1 Cu coordination sphere. Suggestions were made regarding an increase of the T1 redox potential in SLAC, i.e., of Met198 and Thr232 in addition to the axial amino acid Met298. Finally, the results of this work presented a framework for understanding parameters that influence the Type 1 Cu MCO redox potential, useful for an ever-growing range of laccase-based applications. © 2011 American Chemical Society

Counter-ion binding and mobility in the presence of hydrophobic polyions – combining molecular dynamics simulations and NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Druchok, Maksym; Malikova, Natalie; Rollet, Anne-Laure

Counter-ion binding and mobility in aqueous solutions of partially hydrophobic ionene oligoions is studied here by a combination of all-atomic molecular dynamics (MD) simulations and NMR ({sup 19}F and {sup 81}Br nuclei) measurements. We present results for 12, 12–ionenes in the presence of different halide ions (F{sup −}, Cl{sup −}, Br{sup −} and I{sup −}), as well as their mixtures; the latter allowing us to probe counter-ion selectivity of these oligoions. We consolidate both structural and dynamic information, in particular simulated radial distribution functions and average residence times of counter-ions in the vicinity of ionenes and NMR data in themore » form of counter-ion chemical shift and self-diffusion coefficients. On one hand, previously reported enthalpy of dilution and mixing measurements show a reverse counter-ion sequence for 12, 12–ionenes with respect to their less hydrophobic 3, 3– and 6, 6– analogues. On the other hand, the current MD and NMR data, reflecting the counter-ion binding tendencies to the ionene chain, give evidence for the same ordering as that observed by MD for 3, 3–ionenes. This is not seen as a contradiction and can be rationalized on the basis of increasing chain hydrophobicity, which has different consequences for enthalpy and ion-binding. The latter is reflecting free energy changes and as such includes both enthalpic and entropic contributions.« less

Using exploratory regression to identify optimal driving factors for cellular automaton modeling of land use change.

PubMed

Feng, Yongjiu; Tong, Xiaohua

2017-09-22

Defining transition rules is an important issue in cellular automaton (CA)-based land use modeling because these models incorporate highly correlated driving factors. Multicollinearity among correlated driving factors may produce negative effects that must be eliminated from the modeling. Using exploratory regression under pre-defined criteria, we identified all possible combinations of factors from the candidate factors affecting land use change. Three combinations that incorporate five driving factors meeting pre-defined criteria were assessed. With the selected combinations of factors, three logistic regression-based CA models were built to simulate dynamic land use change in Shanghai, China, from 2000 to 2015. For comparative purposes, a CA model with all candidate factors was also applied to simulate the land use change. Simulations using three CA models with multicollinearity eliminated performed better (with accuracy improvements about 3.6%) than the model incorporating all candidate factors. Our results showed that not all candidate factors are necessary for accurate CA modeling and the simulations were not sensitive to changes in statistically non-significant driving factors. We conclude that exploratory regression is an effective method to search for the optimal combinations of driving factors, leading to better land use change models that are devoid of multicollinearity. We suggest identification of dominant factors and elimination of multicollinearity before building land change models, making it possible to simulate more realistic outcomes.

Sensitivity of electrospray molecular dynamics simulations to long-range Coulomb interaction models

NASA Astrophysics Data System (ADS)

Mehta, Neil A.; Levin, Deborah A.

2018-03-01

Molecular dynamics (MD) electrospray simulations of 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF4) ion liquid were performed with the goal of evaluating the influence of long-range Coulomb models on ion emission characteristics. The direct Coulomb (DC), shifted force Coulomb sum (SFCS), and particle-particle particle-mesh (PPPM) long-range Coulomb models were considered in this work. The DC method with a sufficiently large cutoff radius was found to be the most accurate approach for modeling electrosprays, but, it is computationally expensive. The Coulomb potential energy modeled by the DC method in combination with the radial electric fields were found to be necessary to generate the Taylor cone. The differences observed between the SFCS and the DC in terms of predicting the total ion emission suggest that the former should not be used in MD electrospray simulations. Furthermore, the common assumption of domain periodicity was observed to be detrimental to the accuracy of the capillary-based electrospray simulations.

Driver steering dynamics measured in car simulator under a range of visibility and roadmaking conditions

NASA Technical Reports Server (NTRS)

Allen, R. W.; Mcruer, D. T.

1977-01-01

A simulation experiment was conducted to determine the effect of reduced visibility on driver lateral (steering) control. The simulator included a real car cab and a single lane road image projected on a screen six feet in front of the driver. Simulated equations of motion controlled apparent car lane position in response to driver steering actions, wind gusts, and road curvature. Six drivers experienced a range of visibility conditions at various speeds with assorted roadmaking configurations (mark and gap lengths). Driver describing functions were measured and detailed parametric model fits were determined. A pursuit model employing a road curvature feedforward was very effective in explaining driver behavior in following randomly curving roads. Sampled-data concepts were also effective in explaining the combined effects of reduced visibility and intermittent road markings on the driver's dynamic time delay. The results indicate the relative importance of various perceptual variables as the visual input to the driver's steering control process is changed.

Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

DOE PAGES

Radak, Brian K.; Roux, Benoît

2016-10-07

Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance.more » An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.« less

Sensitivity of electrospray molecular dynamics simulations to long-range Coulomb interaction models.

PubMed

Mehta, Neil A; Levin, Deborah A

2018-03-01

Molecular dynamics (MD) electrospray simulations of 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF_{4}) ion liquid were performed with the goal of evaluating the influence of long-range Coulomb models on ion emission characteristics. The direct Coulomb (DC), shifted force Coulomb sum (SFCS), and particle-particle particle-mesh (PPPM) long-range Coulomb models were considered in this work. The DC method with a sufficiently large cutoff radius was found to be the most accurate approach for modeling electrosprays, but, it is computationally expensive. The Coulomb potential energy modeled by the DC method in combination with the radial electric fields were found to be necessary to generate the Taylor cone. The differences observed between the SFCS and the DC in terms of predicting the total ion emission suggest that the former should not be used in MD electrospray simulations. Furthermore, the common assumption of domain periodicity was observed to be detrimental to the accuracy of the capillary-based electrospray simulations.

Simulation of floor heating in a combined solar-biomass system integrated in a public bathhouse located in Marrakech

NASA Astrophysics Data System (ADS)

Krarouch, M.; Hamdi, H.; Lamghari, S.; Outzourhit, A.

2018-05-01

This study was conducted in the framework of the HYBRID-BATH project aiming at improving the energy efficiency of traditional Hammams (Turkish baths) and the reduction of the use of wood energy and therefore of greenhouse gases emissions. The present work focuses on the energetic performance of a two-room Hammam located in Marrakech. The rooms were heated by the ground using a hybrid system Micro-CSP/biomass boiler. The dynamic simulation of the system (Hammam coupled with the hybrid system Micro-CSP/biomass boiler) was conducted using TRNSYS18 software. The parametric study was performed on a Typical Meteorological Year data (TMY). This study is devoted to presenting the results of the dynamic simulation of a part of the Hammam investigated, in order to optimize the underfloor heating system. The models and the results of the simulations will be validated by comparisons with experimental results. The main objective is to optimize the operation of such system and to improve its performance.

Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations.

PubMed

Sultan, Mohammad M; Kiss, Gert; Shukla, Diwakar; Pande, Vijay S

2014-12-09

Given the large number of crystal structures and NMR ensembles that have been solved to date, classical molecular dynamics (MD) simulations have become powerful tools in the atomistic study of the kinetics and thermodynamics of biomolecular systems on ever increasing time scales. By virtue of the high-dimensional conformational state space that is explored, the interpretation of large-scale simulations faces difficulties not unlike those in the big data community. We address this challenge by introducing a method called clustering based feature selection (CB-FS) that employs a posterior analysis approach. It combines supervised machine learning (SML) and feature selection with Markov state models to automatically identify the relevant degrees of freedom that separate conformational states. We highlight the utility of the method in the evaluation of large-scale simulations and show that it can be used for the rapid and automated identification of relevant order parameters involved in the functional transitions of two exemplary cell-signaling proteins central to human disease states.

A Dynamic Health Assessment Approach for Shearer Based on Artificial Immune Algorithm

PubMed Central

Wang, Zhongbin; Xu, Xihua; Si, Lei; Ji, Rui; Liu, Xinhua; Tan, Chao

2016-01-01

In order to accurately identify the dynamic health of shearer, reducing operating trouble and production accident of shearer and improving coal production efficiency further, a dynamic health assessment approach for shearer based on artificial immune algorithm was proposed. The key technologies such as system framework, selecting the indicators for shearer dynamic health assessment, and health assessment model were provided, and the flowchart of the proposed approach was designed. A simulation example, with an accuracy of 96%, based on the collected data from industrial production scene was provided. Furthermore, the comparison demonstrated that the proposed method exhibited higher classification accuracy than the classifiers based on back propagation-neural network (BP-NN) and support vector machine (SVM) methods. Finally, the proposed approach was applied in an engineering problem of shearer dynamic health assessment. The industrial application results showed that the paper research achievements could be used combining with shearer automation control system in fully mechanized coal face. The simulation and the application results indicated that the proposed method was feasible and outperforming others. PMID:27123002

Detection of one-dimensional migration of single self-interstitial atoms in tungsten using high-voltage electron microscopy

PubMed Central

Amino, T.; Arakawa, K.; Mori, H.

2016-01-01

The dynamic behaviour of atomic-size disarrangements of atoms—point defects (self-interstitial atoms (SIAs) and vacancies)—often governs the macroscopic properties of crystalline materials. However, the dynamics of SIAs have not been fully uncovered because of their rapid migration. Using a combination of high-voltage transmission electron microscopy and exhaustive kinetic Monte Carlo simulations, we determine the dynamics of the rapidly migrating SIAs from the formation process of the nanoscale SIA clusters in tungsten as a typical body-centred cubic (BCC) structure metal under the constant-rate production of both types of point defects with high-energy electron irradiation, which must reflect the dynamics of individual SIAs. We reveal that the migration dimension of SIAs is not three-dimensional (3D) but one-dimensional (1D). This result overturns the long-standing and well-accepted view of SIAs in BCC metals and supports recent results obtained by ab-initio simulations. The SIA dynamics clarified here will be one of the key factors to accurately predict the lifetimes of nuclear fission and fusion materials. PMID:27185352

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.

PubMed

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.

A direct evidence of vibrationally delocalized response at ice surface.

PubMed

Ishiyama, Tatsuya; Morita, Akihiro

2014-11-14

Surface-specific vibrational spectroscopic responses at isotope diluted ice and amorphous ice are investigated by molecular dynamics (MD) simulations combined with quantum mechanics/molecular mechanics calculations. The intense response specific to the ordinary crystal ice surface is predicted to be significantly suppressed in the isotopically diluted and amorphous ices, demonstrating the vibrational delocalization at the ordinary ice surface. The collective vibration at the ice surface is also analyzed with varying temperature by the MD simulation.

Enhanced model of gear transmission dynamics for condition monitoring applications: Effects of torque, friction and bearing clearance

NASA Astrophysics Data System (ADS)

Fernandez-del-Rincon, A.; Garcia, P.; Diez-Ibarbia, A.; de-Juan, A.; Iglesias, M.; Viadero, F.

2017-02-01

Gear transmissions remain as one of the most complex mechanical systems from the point of view of noise and vibration behavior. Research on gear modeling leading to the obtaining of models capable of accurately reproduce the dynamic behavior of real gear transmissions has spread out the last decades. Most of these models, although useful for design stages, often include simplifications that impede their application for condition monitoring purposes. Trying to filling this gap, the model presented in this paper allows us to simulate gear transmission dynamics including most of these features usually neglected by the state of the art models. This work presents a model capable of considering simultaneously the internal excitations due to the variable meshing stiffness (including the coupling among successive tooth pairs in contact, the non-linearity linked with the contacts between surfaces and the dissipative effects), and those excitations consequence of the bearing variable compliance (including clearances or pre-loads). The model can also simulate gear dynamics in a realistic torque dependent scenario. The proposed model combines a hybrid formulation for calculation of meshing forces with a non-linear variable compliance approach for bearings. Meshing forces are obtained by means of a double approach which combines numerical and analytical aspects. The methodology used provides a detailed description of the meshing forces, allowing their calculation even when gear center distance is modified due to shaft and bearing flexibilities, which are unavoidable in real transmissions. On the other hand, forces at bearing level were obtained considering a variable number of supporting rolling elements, depending on the applied load and clearances. Both formulations have been developed and applied to the simulation of the vibration of a sample transmission, focusing the attention on the transmitted load, friction meshing forces and bearing preloads.

New Insights into Active Site Conformation Dynamics of E. coli PNP Revealed by Combined H/D Exchange Approach and Molecular Dynamics Simulations.

PubMed

Kazazić, Saša; Bertoša, Branimir; Luić, Marija; Mikleušević, Goran; Tarnowski, Krzysztof; Dadlez, Michal; Narczyk, Marta; Bzowska, Agnieszka

2016-01-01

The biologically active form of purine nucleoside phosphorylase (PNP) from Escherichia coli (EC 2.4.2.1) is a homohexamer unit, assembled as a trimer of dimers. Upon binding of phosphate, neighboring monomers adopt different active site conformations, described as open and closed. To get insight into the functions of the two distinctive active site conformations, virtually inactive Arg24Ala mutant is complexed with phosphate; all active sites are found to be in the open conformation. To understand how the sites of neighboring monomers communicate with each other, we have combined H/D exchange (H/DX) experiments with molecular dynamics (MD) simulations. Both methods point to the mobility of the enzyme, associated with a few flexible regions situated at the surface and within the dimer interface. Although H/DX provides an average extent of deuterium uptake for all six hexamer active sites, it was able to indicate the dynamic mechanism of cross-talk between monomers, allostery. Using this technique, it was found that phosphate binding to the wild type (WT) causes arrest of the molecular motion in backbone fragments that are flexible in a ligand-free state. This was not the case for the Arg24Ala mutant. Upon nucleoside substrate/inhibitor binding, some release of the phosphate-induced arrest is observed for the WT, whereas the opposite effects occur for the Arg24Ala mutant. MD simulations confirmed that phosphate is bound tightly in the closed active sites of the WT; conversely, in the open conformation of the active site of the WT phosphate is bound loosely moving towards the exit of the active site. In Arg24Ala mutant binary complex Pi is bound loosely, too.

The role of loop ZA and Pro371 in the function of yeast Gcn5p bromodomain revealed through molecular dynamics and experiment.

PubMed

Pizzitutti, Francesco; Giansanti, Andrea; Ballario, Paola; Ornaghi, Prisca; Torreri, Paola; Ciccotti, Giovanni; Filetici, Patrizia

2006-01-01

Biological experiments were combined with molecular dynamics simulations to understand the importance of amino acidic residues present in the bromodomain of the yeast histone acetyltransferase Gcn5p. It was found that residue Pro371 plays an important role in the molecular recognition of the acetylated histone H4 tail by Gcn5p bromodomain. Crystallographic analysis of the complex showed that this residue does not directly interact with the histone substrate. It has been demonstrated that a double mutation Pro371Thr and Met372Ala in the Gcn5p bromodomain impairs chromatin remodeling activity. It is demonstrated here that, in this double mutant and in the fully deleted bromodomain strain, there is lower growth under amino acid deprivation conditions. By in vitro surface plasmon resonance (Biacore) experiments it is shown that the binding affinity of the double mutation to acetyl lysine 16 histone H4 peptide decreases. Molecular dynamics simulations were used to explain this loss in acetyl lysine-Gcn5p bromodomain affinity, in the double mutant. By comparing nanosecond molecular dynamics trajectories of the native as well as the single and doubly mutated bromodomain, it is concluded that the presence of Pro371 is important to the functionality of the Gcn5p bromodomain. In the simulation a point mutation involving this highly conserved residue induced an increase in the flexibility of the ZA loop, which in turn modulated the exposure of the binding pocket to the acetyl lysine. The combined double mutations (Pro371Thr-Met372Ala) not only markedly perturb the motion of the ZA loop but also destabilize the entire structure of the bromodomain. Copyright 2005 John Wiley & Sons, Ltd.

Subject-specific computer simulation model for determining elbow loading in one-handed tennis backhand groundstrokes.

PubMed

King, Mark A; Glynn, Jonathan A; Mitchell, Sean R

2011-11-01

A subject-specific angle-driven computer model of a tennis player, combined with a forward dynamics, equipment-specific computer model of tennis ball-racket impacts, was developed to determine the effect of ball-racket impacts on loading at the elbow for one-handed backhand groundstrokes. Matching subject-specific computer simulations of a typical topspin/slice one-handed backhand groundstroke performed by an elite tennis player were done with root mean square differences between performance and matching simulations of < 0.5 degrees over a 50 ms period starting from ball impact. Simulation results suggest that for similar ball-racket impact conditions, the difference in elbow loading for a topspin and slice one-handed backhand groundstroke is relatively small. In this study, the relatively small differences in elbow loading may be due to comparable angle-time histories at the wrist and elbow joints with the major kinematic differences occurring at the shoulder. Using a subject-specific angle-driven computer model combined with a forward dynamics, equipment-specific computer model of tennis ball-racket impacts allows peak internal loading, net impulse, and shock due to ball-racket impact to be calculated which would not otherwise be possible without impractical invasive techniques. This study provides a basis for further investigation of the factors that may increase elbow loading during tennis strokes.

Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy.

PubMed

Voltz, Karine; Léonard, Jérémie; Touceda, Patricia Tourón; Conyard, Jamie; Chaker, Ziyad; Dejaegere, Annick; Godet, Julien; Mély, Yves; Haacke, Stefan; Stote, Roland H

2016-04-20

Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Design Of Combined Stochastic Feedforward/Feedback Control

NASA Technical Reports Server (NTRS)

Halyo, Nesim

1989-01-01

Methodology accommodates variety of control structures and design techniques. In methodology for combined stochastic feedforward/feedback control, main objectives of feedforward and feedback control laws seen clearly. Inclusion of error-integral feedback, dynamic compensation, rate-command control structure, and like integral element of methodology. Another advantage of methodology flexibility to develop variety of techniques for design of feedback control with arbitrary structures to obtain feedback controller: includes stochastic output feedback, multiconfiguration control, decentralized control, or frequency and classical control methods. Control modes of system include capture and tracking of localizer and glideslope, crab, decrab, and flare. By use of recommended incremental implementation, control laws simulated on digital computer and connected with nonlinear digital simulation of aircraft and its systems.

A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study.

PubMed

Chiappori, Federica; Mattiazzi, Luca; Milanesi, Luciano; Merelli, Ivan

2016-03-02

Phosphorylation is one of the most important post-translational modifications (PTM) employed by cells to regulate several cellular processes. Studying the effects of phosphorylations on protein structures allows to investigate the modulation mechanisms of several proteins including chaperones, like the small HSPs, which display different multimeric structures according to the phosphorylation of a few serine residues. In this context, the proposed study is aimed at finding a method to correlate different PTM patterns (in particular phosphorylations at the monomers interface of multimeric complexes) with the dynamic behaviour of the complex, using physicochemical parameters derived from molecular dynamics simulations in the timescale of nanoseconds. We have developed a methodology relying on computing nine physicochemical parameters, derived from the analysis of short MD simulations, and combined with N identifiers that characterize the PTMs of the analysed protein. The nine general parameters were validated on three proteins, with known post-translational modified conformation and unmodified conformation. Then, we applied this approach to the case study of αB-Crystallin, a chaperone which multimeric state (up to 40 units) is supposed to be controlled by phosphorylation of Ser45 and Ser59. Phosphorylation of serines at the dimer interface induces the release of hexamers, the active state of αB-Crystallin. 30 ns of MD simulation were obtained for each possible combination of dimer phosphorylation state and average values of structural, dynamic, energetic and functional features were calculated on the equilibrated portion of the trajectories. Principal Component Analysis was applied to the parameters and the first five Principal Components, which summed up to 84 % of the total variance, were finally considered. The validation of this approach on multimeric proteins, which structures were known both modified and unmodified, allowed us to propose a new approach that can be used to predict the impact of PTM patterns in multi-modified proteins using data collected from short molecular dynamics simulations. Analysis on the αB-Crystallin case study clusters together all-P dimers with all-P hexamers and no-P dimer with no-P hexamer and results suggest a great influence of Ser59 phosphorylation on chain B.

Molecular dynamics simulations of site point mutations in the TPR domain of cyclophilin 40 identify conformational states with distinct dynamic and enzymatic properties

NASA Astrophysics Data System (ADS)

Gur, Mert; Blackburn, Elizabeth A.; Ning, Jia; Narayan, Vikram; Ball, Kathryn L.; Walkinshaw, Malcolm D.; Erman, Burak

2018-04-01

Cyclophilin 40 (Cyp40) is a member of the immunophilin family that acts as a peptidyl-prolyl-isomerase enzyme and binds to the heat shock protein 90 (Hsp90). Its structure comprises an N-terminal cyclophilin domain and a C-terminal tetratricopeptide (TPR) domain. Cyp40 is overexpressed in prostate cancer and certain T-cell lymphomas. The groove for Hsp90 binding on the TPR domain includes residues Lys227 and Lys308, referred to as the carboxylate clamp, and is essential for Cyp40-Hsp90 binding. In this study, the effect of two mutations, K227A and K308A, and their combinative mutant was investigated by performing a total of 5.76 μs of all-atom molecular dynamics (MD) simulations in explicit solvent. All simulations, except the K308A mutant, were found to adopt two distinct (extended or compact) conformers defined by different cyclophilin-TPR interdomain distances. The K308A mutant was only observed in the extended form which is observed in the Cyp40 X-ray structure. The wild-type, K227A, and combined mutant also showed bimodal distributions. The experimental melting temperature, Tm, values of the mutants correlate with the degree of compactness with the K308A extended mutant having a marginally lower melting temperature. Another novel measure of compactness determined from the MD data, the "coordination shell volume," also shows a direct correlation with Tm. In addition, the MD simulations show an allosteric effect with the mutations in the remote TPR domain having a pronounced effect on the molecular motions of the enzymatic cyclophilin domain which helps rationalise the experimentally observed increase in enzyme activity measured for all three mutations.

Linking well-tempered metadynamics simulations with experiments.

PubMed

Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele

2010-05-19

Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm. Quantitative comparison with experimental data is thus possible. Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering approach and comparing the reconstructed nuclear magnetic resonance scalar couplings with experimental data. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Role of flexural stiffness of leukocyte microvilli in adhesion dynamics

NASA Astrophysics Data System (ADS)

Wu, Tai-Hsien; Qi, Dewei

2018-03-01

Previous work reported that microvillus deformation has an important influence on dynamics of cell adhesion. However, the existing studies were limited to the extensional deformation of microvilli and did not consider the effects of their bending deformation on cell adhesion. This Rapid Communication investigates the effects of flexural stiffness of microvilli on the rolling process related to adhesion of leukocytes by using a lattice-Boltzmann lattice-spring method (LLM) combined with adhesive dynamics (AD) simulations. The simulation results reveal that the flexural stiffness of microvilli and their bending deformation have a profound effect on rolling velocity and adhesive forces. As the flexural stiffness of the microvilli decreases, their bending angles increase, resulting in an increase in the number of receptor-ligand bonds and adhesive bonding force and a decrease in the rolling velocity of leukocytes. The effects of flexural stiffness on deformation and adhesion represent crucial factors involved in cell adhesion.

Phonon thermal properties of graphene on h-BN from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zou, Ji-Hang; Cao, Bing-Yang

2017-03-01

Phonon thermal properties of graphene on hexagonal boron nitride are investigated by the molecular dynamics simulations combined with lattice dynamics theory. It is found that the dispersion curves have minor changes for supported graphene because the interlayer coupling is too weak to shift the harmonic phonon properties. The ZA and ZO phonon lifetimes are significantly reduced in supported graphene due to the breakdown of the symmetry-based selection rule. The dominant mean free path (MFP) of graphene is reduced from 90-800 nm to 60-500 nm at 300 K. The mode thermal conductivities of free and supported graphene are 3517 W/ (m.K) and 2200 W/ (m.K) at 300 K, respectively. The thermal conductivity of supported graphene decreases by about 37.4% due to the large reduction of flexural phonon lifetimes, and the relative contribution of flexural modes decreases from 35.0% to 16.7%.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fernandez-Gutierrez, Sulmer, E-mail: sulmer.a.fernandez.gutierrez@intel.com; Browning, Jim; Lin, Ming-Chieh

Phase-control of a magnetron is studied via simulation using a combination of a continuous current source and a modulated current source. The addressable, modulated current source is turned ON and OFF at the magnetron operating frequency in order to control the electron injection and the spoke phase. Prior simulation work using a 2D model of a Rising Sun magnetron showed that the use of 100% modulated current controlled the magnetron phase and allowed for dynamic phase control. In this work, the minimum fraction of modulated current source needed to achieve a phase control is studied. The current fractions (modulated versusmore » continuous) were varied from 10% modulated current to 100% modulated current to study the effects on phase control. Dynamic phase-control, stability, and start up time of the device were studied for all these cases showing that with 10% modulated current and 90% continuous current, a phase shift of 180° can be achieved demonstrating dynamic phase control.« less

Water dynamics during the association of hiv capsid proteins studied by all-atom simulations

NASA Astrophysics Data System (ADS)

Yu, Naiyin; Hagan, Michael

2012-02-01

The C-terminal domain of the HIV-1 capsid protein (CA-C) plays an important role in the assembly of the mature capsid. We have used molecular dynamics simulations combined with enhanced sampling methods to study the association of two CA-C proteins in atomistic detail. In this talk we will discuss the dynamics of water during the association process. In particular, we will show that that water in the interfacial region does not undergo a liquid-vapor transition (de-wetting) during association of wild type CA-C. However, mutation of some hydrophilic residues does lead to a dewetting transition. We discuss the relationship between the arrangement of hydrophilic and hydrophobic residues and dewetting during protein association. For the HIV capsid protein, the arrangement of hydrophilic residues contributes to maintaining weak interactions, which are crucial for successful assembly.

Automatic detection of slight parameter changes associated to complex biomedical signals using multiresolution q-entropy1.

PubMed

Torres, M E; Añino, M M; Schlotthauer, G

2003-12-01

It is well known that, from a dynamical point of view, sudden variations in physiological parameters which govern certain diseases can cause qualitative changes in the dynamics of the corresponding physiological process. The purpose of this paper is to introduce a technique that allows the automated temporal localization of slight changes in a parameter of the law that governs the nonlinear dynamics of a given signal. This tool takes, from the multiresolution entropies, the ability to show these changes as statistical variations at each scale. These variations are held in the corresponding principal component. Appropriately combining these techniques with a statistical changes detector, a complexity change detection algorithm is obtained. The relevance of the approach, together with its robustness in the presence of moderate noise, is discussed in numerical simulations and the automatic detector is applied to real and simulated biological signals.

MONALISA for stochastic simulations of Petri net models of biochemical systems.

PubMed

Balazki, Pavel; Lindauer, Klaus; Einloft, Jens; Ackermann, Jörg; Koch, Ina

2015-07-10

The concept of Petri nets (PN) is widely used in systems biology and allows modeling of complex biochemical systems like metabolic systems, signal transduction pathways, and gene expression networks. In particular, PN allows the topological analysis based on structural properties, which is important and useful when quantitative (kinetic) data are incomplete or unknown. Knowing the kinetic parameters, the simulation of time evolution of such models can help to study the dynamic behavior of the underlying system. If the number of involved entities (molecules) is low, a stochastic simulation should be preferred against the classical deterministic approach of solving ordinary differential equations. The Stochastic Simulation Algorithm (SSA) is a common method for such simulations. The combination of the qualitative and semi-quantitative PN modeling and stochastic analysis techniques provides a valuable approach in the field of systems biology. Here, we describe the implementation of stochastic analysis in a PN environment. We extended MONALISA - an open-source software for creation, visualization and analysis of PN - by several stochastic simulation methods. The simulation module offers four simulation modes, among them the stochastic mode with constant firing rates and Gillespie's algorithm as exact and approximate versions. The simulator is operated by a user-friendly graphical interface and accepts input data such as concentrations and reaction rate constants that are common parameters in the biological context. The key features of the simulation module are visualization of simulation, interactive plotting, export of results into a text file, mathematical expressions for describing simulation parameters, and up to 500 parallel simulations of the same parameter sets. To illustrate the method we discuss a model for insulin receptor recycling as case study. We present a software that combines the modeling power of Petri nets with stochastic simulation of dynamic processes in a user-friendly environment supported by an intuitive graphical interface. The program offers a valuable alternative to modeling, using ordinary differential equations, especially when simulating single-cell experiments with low molecule counts. The ability to use mathematical expressions provides an additional flexibility in describing the simulation parameters. The open-source distribution allows further extensions by third-party developers. The software is cross-platform and is licensed under the Artistic License 2.0.

Moment Lyapunov Exponent and Stochastic Stability of Binary Airfoil under Combined Harmonic and Non-Gaussian Colored Noise Excitations

NASA Astrophysics Data System (ADS)

Hu, D. L.; Liu, X. B.

Both periodic loading and random forces commonly co-exist in real engineering applications. However, the dynamic behavior, especially dynamic stability of systems under parametric periodic and random excitations has been reported little in the literature. In this study, the moment Lyapunov exponent and stochastic stability of binary airfoil under combined harmonic and non-Gaussian colored noise excitations are investigated. The noise is simplified to an Ornstein-Uhlenbeck process by applying the path-integral method. Via the singular perturbation method, the second-order expansions of the moment Lyapunov exponent are obtained, which agree well with the results obtained by the Monte Carlo simulation. Finally, the effects of the noise and parametric resonance (such as subharmonic resonance and combination additive resonance) on the stochastic stability of the binary airfoil system are discussed.

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations.

PubMed

Heidari, Zahra; Roe, Daniel R; Galindo-Murillo, Rodrigo; Ghasemi, Jahan B; Cheatham, Thomas E

2016-07-25

Long time scale molecular dynamics (MD) simulations of biological systems are becoming increasingly commonplace due to the availability of both large-scale computational resources and significant advances in the underlying simulation methodologies. Therefore, it is useful to investigate and develop data mining and analysis techniques to quickly and efficiently extract the biologically relevant information from the incredible amount of generated data. Wavelet analysis (WA) is a technique that can quickly reveal significant motions during an MD simulation. Here, the application of WA on well-converged long time scale (tens of μs) simulations of a DNA helix is described. We show how WA combined with a simple clustering method can be used to identify both the physical and temporal locations of events with significant motion in MD trajectories. We also show that WA can not only distinguish and quantify the locations and time scales of significant motions, but by changing the maximum time scale of WA a more complete characterization of these motions can be obtained. This allows motions of different time scales to be identified or ignored as desired.

Dynamics of Magnetopause Reconnection in Response to Variable Solar Wind Conditions

NASA Astrophysics Data System (ADS)

Berchem, J.; Richard, R. L.; Escoubet, C. P.; Pitout, F.

2017-12-01

Quantifying the dynamics of magnetopause reconnection in response to variable solar wind driving is essential to advancing our predictive understanding of the interaction of the solar wind/IMF with the magnetosphere. To this end we have carried out numerical studies that combine global magnetohydrodynamic (MHD) and Large-Scale Kinetic (LSK) simulations to identify and understand the effects of solar wind/IMF variations. The use of the low dissipation, high resolution UCLA MHD code incorporating a non-linear local resistivity allows the representation of the global configuration of the dayside magnetosphere while the use of LSK ion test particle codes with distributed particle detectors allows us to compare the simulation results with spacecraft observations such as ion dispersion signatures observed by the Cluster spacecraft. We present the results of simulations that focus on the impacts of relatively simple solar wind discontinuities on the magnetopause and examine how the recent history of the interaction of the magnetospheric boundary with solar wind discontinuities can modify the dynamics of magnetopause reconnection in response to the solar wind input.

Investigations of Takeout proteins' ligand binding and release mechanism using molecular dynamics simulation.

PubMed

Zhang, Huijing; Yu, Hui; Zhao, Xi; Liu, Xiaoguang; Feng, Xianli; Huang, Xuri

2017-05-01

Takeout (To) proteins exist in a diverse range of insect species. They are involved in many important processes of insect physiology and behaviors. As the ligand carriers, To proteins can transport the small molecule to the target tissues. However, ligand release mechanism of To proteins is unclear so far. In this contribution, the process and pathway of the ligand binding and release are revealed by conventional molecular dynamics simulation, steered molecular dynamics simulation and umbrella sampling methods. Our results show that the α4-side of the protein is the unique gate for the ligand binding and release. The structural analysis confirms that the internal cavity of the protein has high rigidity, which is in accordance with the recent experimental results. By using the potential of mean force calculations in combination with residue cross correlation calculation, we concluded that the binding between the ligand and To proteins is a process of conformational selection. Furthermore, the conformational changes of To proteins and the hydrophobic interactions both are the key factors for ligand binding and release.

In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations.

PubMed

Gao, Xiaodong; Han, Liping; Ren, Yujie

2016-05-05

Checkpoint kinase 1 (Chk1) is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling, molecular docking, and molecular dynamics simulations. The optimal QSAR models showed significant cross-validated correlation q² values (0.531, 0.726), fitted correlation r² coefficients (higher than 0.90), and standard error of prediction (less than 0.250). These results suggested that the developed models possess good predictive ability. Moreover, molecular docking and molecular dynamics simulations were applied to highlight the important interactions between the ligand and the Chk1 receptor protein. This study shows that hydrogen bonding and electrostatic forces are key interactions that confer bioactivity.

Dissociative electron attachments to ethanol and acetaldehyde: A combined experimental and simulation study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xu-Dong; Xuan, Chuan-Jin; Feng, Wen-Ling

Dissociation dynamics of the temporary negative ions of ethanol and acetaldehyde formed by the low-energy electron attachments is investigated by using the anion velocity map imaging technique and ab initio molecular dynamics simulations. The momentum images of the dominant fragments O{sup −}/OH{sup −} and CH{sub 3}{sup −} are recorded, indicating the low kinetic energies of O{sup −}/OH{sup −} for ethanol while the low and high kinetic energy distributions of O{sup −} ions for acetaldehyde. The CH{sub 3}{sup −} image for acetaldehyde also shows the low kinetic energy. With help of the dynamics simulations, the fragmentation processes are qualitatively clarified. Amore » new cascade dissociation pathway to produce the slow O{sup −} ion via the dehydrogenated intermediate, CH{sub 3}CHO{sup −} (acetaldehyde anion), is proposed for the dissociative electron attachment to ethanol. After the electron attachment to acetaldehyde molecule, the slow CH{sub 3}{sup −} is produced quickly in the two-body dissociation with the internal energy redistributions in different aspects before bond cleavages.« less

Dynamic model based on voltage transfer curve for pattern formation in dielectric barrier glow discharge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Ben; He, Feng; Ouyang, Jiting, E-mail: jtouyang@bit.edu.cn

2015-12-15

Simulation work is very important for understanding the formation of self-organized discharge patterns. Previous works have witnessed different models derived from other systems for simulation of discharge pattern, but most of these models are complicated and time-consuming. In this paper, we introduce a convenient phenomenological dynamic model based on the basic dynamic process of glow discharge and the voltage transfer curve (VTC) to study the dielectric barrier glow discharge (DBGD) pattern. VTC is an important characteristic of DBGD, which plots the change of wall voltage after a discharge as a function of the initial total gap voltage. In the modeling,more » the combined effect of the discharge conditions is included in VTC, and the activation-inhibition effect is expressed by a spatial interaction term. Besides, the model reduces the dimensionality of the system by just considering the integration effect of current flow. All these greatly facilitate the construction of this model. Numerical simulations turn out to be in good accordance with our previous fluid modeling and experimental result.« less

Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway

NASA Astrophysics Data System (ADS)

Harada, Ryuhei; Kitao, Akio

2013-07-01

Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular simulation method to generate conformational transition pathway under the condition that a set of "reactant" and "product" structures is known a priori. In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the product structure for the next cycle are repeated until the simulated structures move sufficiently close to the product. Folding of 10-residue mini-protein chignolin from the extended to native structures and open-close conformational transition of T4 lysozyme were investigated by PaCS-MD. In both cases, tens of cycles of 100-ps MD were sufficient to reach the product structures, indicating the efficient generation of conformational transition pathway in PaCS-MD with a series of conventional MD without additional external biases. Using the snapshots along the pathway as the initial coordinates, free energy landscapes were calculated by the combination with multiple independent umbrella samplings to statistically elucidate the conformational transition pathways.

PAMAM dendrimers and graphene: Materials for removing aromatic contaminants from water

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeFever, Ryan S.; Geitner, Nicholas K.; Bhattacharya, Priyanka

2015-04-07

We present results from experiments and atomistic molecular dynamics simulations on the association of naphthalene with polyamidoamine (PAMAM) dendrimers and graphene oxide (GrO). Specifically, we investigate 3rd-6th generation (G3-G6) PAMAM dendrimers and GrO with different levels of oxidation. The work is motivated by the potential applications of these materials in removing polycyclic aromatic hydrocarbon contaminants from water. Our experimental results indicate that graphene oxide outperforms dendrimers in removing naphthalene from water. Molecular dynamics simulations suggest that the prominent factors driving naphthalene association to these seemingly disparate materials are similar. Interestingly, we find that cooperative interactions between the naphthalene molecules playmore » a significant role in enhancing their association to the dendrimers and graphene oxide. Our findings highlight that while selection of appropriate materials is important, the interactions between the contaminants themselves can also be important in governing the effectiveness of a given material. The combined use of experiments and molecular dynamics simulations allows us to comment on the possible factors resulting in better performance of graphene oxide in removing naphthalene from water.« less

Simulation of meso-damage of refractory based on cohesion model and molecular dynamics method

NASA Astrophysics Data System (ADS)

Zhao, Jiuling; Shang, Hehao; Zhu, Zhaojun; Zhang, Guoxing; Duan, Leiguang; Sun, Xinya

2018-06-01

In order to describe the meso-damage of the refractories more accurately, and to study of the relationship between the mesostructured of the refractories and the macro-mechanics, this paper takes the magnesia-carbon refractories as the research object and uses the molecular dynamics method to instead the traditional sequential algorithm to establish the meso-particles filling model including small and large particles. Finally, the finite element software-ABAQUS is used to conducts numerical simulation on the meso-damage evolution process of refractory materials. From the results, the process of initiation and propagation of microscopic interface cracks can be observed intuitively, and the macroscopic stress-strain curve of the refractory material is obtained. The results show that the combination of molecular dynamics modeling and the use of Python in the interface to insert the cohesive element numerical simulation, obtaining of more accurate interface parameters through parameter inversion, can be more accurate to observe the interface of the meso-damage evolution process and effective to consider the effect of the mesostructured of the refractory material on its macroscopic mechanical properties.

Femtosecond excitation tuning and site energy memory of population transfer in poly(p-phenylenevinylene): Gated luminescence experiments and simulation

NASA Astrophysics Data System (ADS)

Sperling, J.; Milota, F.; Tortschanoff, A.; Warmuth, Ch.; Mollay, B.; Bässler, H.; Kauffmann, H. F.

2002-12-01

We present a comprehensive experimental and computational study on fs-relaxational dynamics of optical excitations in the conjugated polymer poly(p-phenylenevinylene) (PPV) under selective excitation tuning conditions into the long-wavelength, low-vibrational S1ν=0-density-of-states (DOS). The dependence of single-wavelength luminescence kinetics and time-windowed spectral transients on distinct, initial excitation boundaries at 1.4 K and at room temperature was measured applying the luminescence up-conversion technique. The typical energy-dispersive intra-DOS energy transfer was simulated by a combination of static Monte Carlo method with a dynamical algorithm for solving the energy-space transport Master-Equation in population-space. For various, selective excitations that give rise to specific S1-population distributions in distinct spatial and energetic subspaces inside the DOS, simulations confirm the experimental results and show that the subsequent, energy-dissipative, multilevel relaxation is hierarchically constrained, and reveals a pronounced site-energy memory effect with a migration-threshold, characteristic of the (dressed) excitation dynamics in the disordered PPV many-body system.

PAMAM dendrimers and graphene: materials for removing aromatic contaminants from water.

PubMed

DeFever, Ryan S; Geitner, Nicholas K; Bhattacharya, Priyanka; Ding, Feng; Ke, Pu Chun; Sarupria, Sapna

2015-04-07

We present results from experiments and atomistic molecular dynamics simulations on the remediation of naphthalene by polyamidoamine (PAMAM) dendrimers and graphene oxide (GrO). Specifically, we investigate 3rd-6th generation (G3-G6) PAMAM dendrimers and GrO with different levels of oxidation. The work is motivated by the potential applications of these emerging nanomaterials in removing polycyclic aromatic hydrocarbon contaminants from water. Our experimental results indicate that GrO outperforms dendrimers in removing naphthalene from water. Molecular dynamics simulations suggest that the prominent factors driving naphthalene association to these seemingly disparate materials are similar. Interestingly, we find that cooperative interactions between the naphthalene molecules play a significant role in enhancing their association to the dendrimers and GrO. Our findings highlight that while selection of appropriate materials is important, the interactions between the contaminants themselves can also be important in governing the effectiveness of a given material. The combined use of experiments and molecular dynamics simulations allows us to comment on the possible factors resulting in better performance of GrO in removing polyaromatic contaminants from water.

Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations.

PubMed

Duboué-Dijon, Elise; Mason, Philip E; Fischer, Henry E; Jungwirth, Pavel

2018-04-05

Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H 2 O and D 2 O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg 2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing quantitatively.

Multi-Conformer Ensemble Docking to Difficult Protein Targets

DOE PAGES

Ellingson, Sally R.; Miao, Yinglong; Baudry, Jerome; ...

2014-09-08

We investigate large-scale ensemble docking using five proteins from the Directory of Useful Decoys (DUD, dud.docking.org) for which docking to crystal structures has proven difficult. Molecular dynamics trajectories are produced for each protein and an ensemble of representative conformational structures extracted from the trajectories. Docking calculations are performed on these selected simulation structures and ensemble-based enrichment factors compared with those obtained using docking in crystal structures of the same protein targets or random selection of compounds. We also found simulation-derived snapshots with improved enrichment factors that increased the chemical diversity of docking hits for four of the five selected proteins.more » A combination of all the docking results obtained from molecular dynamics simulation followed by selection of top-ranking compounds appears to be an effective strategy for increasing the number and diversity of hits when using docking to screen large libraries of chemicals against difficult protein targets.« less

An evaluation of noise reduction algorithms for particle-based fluid simulations in multi-scale applications

NASA Astrophysics Data System (ADS)

Zimoń, M. J.; Prosser, R.; Emerson, D. R.; Borg, M. K.; Bray, D. J.; Grinberg, L.; Reese, J. M.

2016-11-01

Filtering of particle-based simulation data can lead to reduced computational costs and enable more efficient information transfer in multi-scale modelling. This paper compares the effectiveness of various signal processing methods to reduce numerical noise and capture the structures of nano-flow systems. In addition, a novel combination of these algorithms is introduced, showing the potential of hybrid strategies to improve further the de-noising performance for time-dependent measurements. The methods were tested on velocity and density fields, obtained from simulations performed with molecular dynamics and dissipative particle dynamics. Comparisons between the algorithms are given in terms of performance, quality of the results and sensitivity to the choice of input parameters. The results provide useful insights on strategies for the analysis of particle-based data and the reduction of computational costs in obtaining ensemble solutions.