Effect of Single-Electron Interface Trapping in Decanano MOSFETs: A 3D Atomistic Simulation Study

Science.gov (United States)

Asenov, Asen; Balasubramaniam, R.; Brown, A. R.; Davies, J. H.

2000-01-01

We study the effect of trapping/detrapping of a single-electron in interface states in the channel of n-type MOSFETs with decanano dimensions using 3D atomistic simulation techniques. In order to highlight the basic dependencies, the simulations are carried out initially assuming continuous doping charge, and discrete localized charge only for the trapped electron. The dependence of the random telegraph signal (RTS) amplitudes on the device dimensions and on the position of the trapped charge in the channel are studied in detail. Later, in full-scale, atomistic simulations assuming discrete charge for both randomly placed dopants and the trapped electron, we highlight the importance of current percolation and of traps with strategic position where the trapped electron blocks a dominant current path.

Atomistic simulations in Si processing: Bridging the gap between atoms and experiments

International Nuclear Information System (INIS)

Marques, Luis A.; Pelaz, Lourdes; Lopez, Pedro; Aboy, Maria; Santos, Ivan; Barbolla, Juan

2005-01-01

With devices shrinking to nanometric scale, process simulation tools have to shift from continuum models to an atomistic description of the material. However, the limited sizes and time scales accessible for detailed atomistic techniques usually lead to the difficult task of relating the information obtained from simulations to experimental data. The solution consists of the use of a hierarchical simulation scheme: more fundamental techniques are employed to extract parameters and models that are then feed into less detailed simulators which allow direct comparison with experiments. This scheme will be illustrated with the modeling of the amorphization and recrystallization of Si, which has been defined as a key challenge in the last edition of the International Technology Roadmap for Semiconductors. The model is based on the bond defect or IV pair, which is used as the building block of the amorphous phase. The properties of this defect have been studied using ab initio methods and classical molecular dynamics techniques. It is shown that the recombination of this defect depends on the surrounding bond defects, which accounts for the cooperative nature of the amorphization and recrystallization processes. The implementation of this model in a kinetic Monte Carlo code allows extracting data directly comparable with experiments. This approach provides physical insight on the amorphization and recrystallization mechanisms and a tool for the optimization of solid-phase epitaxial-related processes

DoGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

DEFF Research Database (Denmark)

Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector

2017-01-01

Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would...... be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools...

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

Science.gov (United States)

Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

2009-01-01

Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

Atomistic Monte Carlo simulation of lipid membranes

DEFF Research Database (Denmark)

Wüstner, Daniel; Sklenar, Heinz

2014-01-01

Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction...... of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol....

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

Science.gov (United States)

Knoch, Fabian; Schäfer, Ken; Diezemann, Gregor; Speck, Thomas

2018-01-01

We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

Spatio-Temporal Process Simulation of Dam-Break Flood Based on SPH

Science.gov (United States)

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.

Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

2013-10-01

In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.

A new scaling approach for the mesoscale simulation of magnetic domain structures using Monte Carlo simulations

Energy Technology Data Exchange (ETDEWEB)

Radhakrishnan, B., E-mail: radhakrishnb@ornl.gov; Eisenbach, M.; Burress, T.A.

2017-06-15

Highlights: • Developed new scaling technique for dipole–dipole interaction energy. • Developed new scaling technique for exchange interaction energy. • Used scaling laws to extend atomistic simulations to micrometer length scale. • Demonstrated transition from mono-domain to vortex magnetic structure. • Simulated domain wall width and transition length scale agree with experiments. - Abstract: A new scaling approach has been proposed for the spin exchange and the dipole–dipole interaction energy as a function of the system size. The computed scaling laws are used in atomistic Monte Carlo simulations of magnetic moment evolution to predict the transition from single domain to a vortex structure as the system size increases. The width of a 180° – domain wall extracted from the simulated structures is in close agreement with experimentally values for an F–Si alloy. The transition size from a single domain to a vortex structure is also in close agreement with theoretically predicted and experimentally measured values for Fe.

Atomistic simulations of Mg-Cu metallic glasses: Mechanical properties

DEFF Research Database (Denmark)

Bailey, Nicholas; Schiøtz, Jakob; Jacobsen, Karsten Wedel

2004-01-01

The atomistic mechanisms of plastic deformation in amorphous metals are far from being understood. We have derived potential parameters for molecular dynamics simulations of Mg-Cu amorphous alloys using the Effective Medium Theory. We have simulated the formation of alloys by cooling from the melt...

Comparative simulations of microjetting using atomistic and continuous approaches in the presence of viscosity and surface tension

Science.gov (United States)

Durand, O.; Jaouen, S.; Soulard, L.; Heuzé, O.; Colombet, L.

2017-10-01

We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations with systems containing up to 700 × 106 atoms. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and the equation of state is calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with very good agreement the profiles, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes also exhibit a similar fragmentation phenomenology of the metallic liquid sheets ejected, although the fragmentation seed is different. We show in particular, that it depends on the mesh size in the continuous approach.

Atomistic Monte Carlo Simulation of Lipid Membranes

Directory of Open Access Journals (Sweden)

Daniel Wüstner

2014-01-01

Full Text Available Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA for the phospholipid dipalmitoylphosphatidylcholine (DPPC. We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.

Atomistic simulations of contact area and conductance at nanoscale interfaces.

Science.gov (United States)

Hu, Xiaoli; Martini, Ashlie

2017-11-09

Atomistic simulations were used to study conductance across the interface between a nanoscale gold probe and a graphite surface with a step edge. Conductance on the graphite terrace was observed to increase with load and be approximately proportional to contact area calculated from the positions of atoms in the interface. The relationship between area and conductance was further explored by varying the position of the contact relative to the location of the graphite step edge. These simulations reproduced a previously-reported current dip at step edges measured experimentally and the trend was explained by changes in both contact area and the distribution of distances between atoms in the interface. The novel approach reported here provides a foundation for future studies of the fundamental relationships between conductance, load and surface topography at the atomic scale.

Definition and detection of contact in atomistic simulations

NARCIS (Netherlands)

Solhjoo, Soheil; Vakis, Antonis I.

In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,

Definition and detection of contact in atomistic simulations

NARCIS (Netherlands)

Solhjoo, Soheil; Vakis, Antonis I.

2015-01-01

In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,

Quantum-based Atomistic Simulation of Transition Metals

International Nuclear Information System (INIS)

Moriarty, J A; Benedict, L X; Glosli, J N; Hood, R Q; Orlikowski, D A; Patel, M V; Soderlind, P; Streitz, F H; Tang, M; Yang, L H

2005-01-01

First-principles generalized pseudopotential theory (GPT) provides a fundamental basis for transferable multi-ion interatomic potentials in d-electron transition metals within density-functional quantum mechanics. In mid-period bcc metals, where multi-ion angular forces are important to structural properties, simplified model GPT or MGPT potentials have been developed based on canonical d bands to allow analytic forms and large-scale atomistic simulations. Robust, advanced-generation MGPT potentials have now been obtained for Ta and Mo and successfully applied to a wide range of structural, thermodynamic, defect and mechanical properties at both ambient and extreme conditions of pressure and temperature. Recent algorithm improvements have also led to a more general matrix representation of MGPT beyond canonical bands allowing increased accuracy and extension to f-electron actinide metals, an order of magnitude increase in computational speed, and the current development of temperature-dependent potentials

Full-Scale Approximations of Spatio-Temporal Covariance Models for Large Datasets

KAUST Repository

Zhang, Bohai

2014-01-01

Various continuously-indexed spatio-temporal process models have been constructed to characterize spatio-temporal dependence structures, but the computational complexity for model fitting and predictions grows in a cubic order with the size of dataset and application of such models is not feasible for large datasets. This article extends the full-scale approximation (FSA) approach by Sang and Huang (2012) to the spatio-temporal context to reduce computational complexity. A reversible jump Markov chain Monte Carlo (RJMCMC) algorithm is proposed to select knots automatically from a discrete set of spatio-temporal points. Our approach is applicable to nonseparable and nonstationary spatio-temporal covariance models. We illustrate the effectiveness of our method through simulation experiments and application to an ozone measurement dataset.

Atomistic simulations of dislocation processes in copper

DEFF Research Database (Denmark)

Vegge, T.; Jacobsen, K.W.

2002-01-01

We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example......, the stability of screw dislocation dipoles is discussed. We show that the presence of jogs will strongly influence cross slip barriers and dipole stability. We furthermore present some new results on jogged edge dislocations and edge dislocation dipoles. The jogs are found to be extended, and simulations...

Multi-scale modelling of ions in solution: from atomistic descriptions to chemical engineering

International Nuclear Information System (INIS)

Molina, J.J.

2011-01-01

Ions in solution play a fundamental role in many physical, chemical, and biological processes. The PUREX process used in the nuclear industry to the treatment of spent nuclear fuels is considered as an example. For industrial applications these systems are usually described using simple analytical models which are fitted to reproduce the available experimental data. In this work, we propose a multi-scale coarse graining procedure to derive such models from atomistic descriptions. First, parameters for classical force-fields of ions in solution are extracted from ab-initio calculations. Effective (McMillan-Mayer) ion-ion potentials are then derived from radial distribution functions measured in classical molecular dynamics simulations, allowing us to define an implicit solvent model of electrolytes. Finally, perturbation calculations are performed to define the best possible representation for these systems, in terms of charged hard-sphere models. Our final model is analytical and contains no free 'fitting' parameters. It shows good agreement with the exact results obtained from Monte-Carlo simulations for the thermodynamic and structural properties. Development of a similar model for the electrolyte viscosity, from information derived from atomistic descriptions, is also introduced. (author)

Quantum Corrections to the 'Atomistic' MOSFET Simulations

Science.gov (United States)

Asenov, Asen; Slavcheva, G.; Kaya, S.; Balasubramaniam, R.

2000-01-01

We have introduced in a simple and efficient manner quantum mechanical corrections in our 3D 'atomistic' MOSFET simulator using the density gradient formalism. We have studied in comparison with classical simulations the effect of the quantum mechanical corrections on the simulation of random dopant induced threshold voltage fluctuations, the effect of the single charge trapping on interface states and the effect of the oxide thickness fluctuations in decanano MOSFETs with ultrathin gate oxides. The introduction of quantum corrections enhances the threshold voltage fluctuations but does not affect significantly the amplitude of the random telegraph noise associated with single carrier trapping. The importance of the quantum corrections for proper simulation of oxide thickness fluctuation effects has also been demonstrated.

Ionic diffusion in quartz studied by transport measurements, SIMS and atomistic simulations

International Nuclear Information System (INIS)

Sartbaeva, Asel; Wells, Stephen A; Redfern, Simon A T; Hinton, Richard W; Reed, Stephen J B

2005-01-01

Ionic diffusion in the quartz-β-eucryptite system is studied by DC transport measurements, SIMS and atomistic simulations. Transport data show a large transient increase in ionic current at the α-β phase transition of quartz (the Hedvall effect). The SIMS data indicate two diffusion processes, one involving rapid Li + motion and the other involving penetration of Al and Li atoms into quartz at the phase transition. Atomistic simulations explain why the fine microstructure of twin domain walls in quartz near the transition does not hinder Li + diffusion

Atomistic simulation of solid solution hardening in Mg/Al alloys: Examination of composition scaling and thermo-mechanical relationships

International Nuclear Information System (INIS)

Yi, Peng; Cammarata, Robert C.; Falk, Michael L.

2016-01-01

Dislocation mobility in a solid solution was studied using atomistic simulations of an Mg/Al system. The critical resolved shear stress (CRSS) for the dislocations on the basal plane was calculated at temperatures from 0 K to 500 K with solute concentrations from 0 to 7 at%, and with four different strain rates. Solute hardening of the CRSS is decomposed into two contributions: one scales with c 2/3 , where c is the solute concentration, and the other scales with c 1 . The former was consistent with the Labusch model for local solute obstacles, and the latter was related to the athermal plateau stress due to the long range solute effect. A thermo-mechanical model was then used to analyze the temperature and strain rate dependences of the CRSS, and it yielded self-consistent and realistic results. The scaling laws were confirmed and the thermo-mechanical model was successfully parameterized using experimental measurements of the CRSS for Mg/Al alloys under quasi-static conditions. The predicted strain rate sensitivity from the experimental measurements of the CRSS is in reasonable agreement with separate mechanical tests. The concentration scaling and the thermo-mechanical relationships provide a potential tool to analytically relate the structural and thermodynamic parameters on the microscopic level with the macroscopic mechanical properties arising from dislocation mediated deformation.

Atomistic simulations of bulk, surface and interfacial polymer properties

Science.gov (United States)

Natarajan, Upendra

In chapter I, quasi-static molecular mechanics based simulations are used to estimate the activation energy of phenoxy rings flips in the amorphous region of a semicrystalline polyimide. Intra and intermolecular contributions to the flip activation energy, the torsional cooperativity accompanying the flip, and the effect of the flip on the motion in the glassy bulk state, are looked at. Also, comparison of the weighted mean activation energy is made with experimental data from solid state NMR measurements; the simulated value being 17.5 kcal/mol., while the experimental value was observed to be 10.5 kcal/mol. Chapter II deals with construction of random copolymer thin films of styrene-butadiene (SB) and styrene-butadiene-acrylonitrile (SBA). The structure and properties of the free surfaces presented by these thin films are analysed by, the atom mass density profiles, backbone bond orientation function, and the spatial distribution of acrylonitrile groups and styrene rings. The surface energies of SB and SBA are calculated using an atomistic equation and are compared with experimental data in the literature. In chapter III, simulations of polymer-polymer interfaces between like and unlike polymers, specifically cis-polybutadiene (PBD) and atatic polypropylene (PP), are presented. The structure of an incompatible polymer-polymer interface, and the estimation of the thermodynamic work of adhesion and interfacial energy between different incompatible polymers, form the focus here. The work of adhesion is calculated using an atomistic equation and is further used in a macroscopic equation to estimate the interfacial energy. The interfacial energy is compared with typical values for other immiscible systems in the literature. The interfacial energy compared very well with interfacial energy values for a few other immiscible hydrocarbon pairs. In chapter IV, the study proceeds to look at the interactions between nonpolar and polar small molecules with SB and SBA thin

Atomistic modeling of nanowires, small-scale fatigue damage in cast magnesium, and materials for MEMS

Energy Technology Data Exchange (ETDEWEB)

Dunn, Martin L. [Univ. of Colorado, Boulder, CO (United States); Talmage, Mellisa J. [Univ. of Colorado, Boulder, CO (United States); McDowell, David L. [Georgia Inst. of Technology, Atlanta, GA (United States); West, Neil [Univ. of Colorado, Boulder, CO (United States); Gullett, Philip Michael [Mississippi State Univ., Mississippi State, MS (United States); Miller, David C. [Univ. of Colorado, Boulder, CO (United States); Spark, Kevin [Univ. of Colorado, Boulder, CO (United States); Diao, Jiankuai [Univ. of Colorado, Boulder, CO (United States); Horstemeyer, Mark F. [Mississippi State Univ., Mississippi State, MS (United States); Zimmerman, Jonathan A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gall, K. [Georgia Inst. of Technology, Atlanta, GA (United States)

2006-10-01

Lightweight and miniaturized weapon systems are driving the use of new materials in design such as microscale materials and ultra low-density metallic materials. Reliable design of future weapon components and systems demands a thorough understanding of the deformation modes in these materials that comprise the components and a robust methodology to predict their performance during service or storage. Traditional continuum models of material deformation and failure are not easily extended to these new materials unless microstructural characteristics are included in the formulation. For example, in LIGA Ni and Al-Si thin films, the physical size is on the order of microns, a scale approaching key microstructural features. For a new potential structural material, cast Mg offers a high stiffness-to-weight ratio, but the microstructural heterogeneity at various scales requires a structure-property continuum model. Processes occurring at the nanoscale and microscale develop certain structures that drive material behavior. The objective of the work presented in this report was to understand material characteristics in relation to mechanical properties at the nanoscale and microscale in these promising new material systems. Research was conducted primarily at the University of Colorado at Boulder to employ tightly coupled experimentation and simulation to study damage at various material size scales under monotonic and cyclic loading conditions. Experimental characterization of nano/micro damage will be accomplished by novel techniques such as in-situ environmental scanning electron microscopy (ESEM), 1 MeV transmission electron microscopy (TEM), and atomic force microscopy (AFM). New simulations to support experimental efforts will include modified embedded atom method (MEAM) atomistic simulations at the nanoscale and single crystal micromechanical finite element simulations. This report summarizes the major research and development accomplishments for the LDRD project

Atomistic simulation of MgO nanowires subject to electromagnetic wave

International Nuclear Information System (INIS)

Wang, Xianqiao; Lee, James D

2010-01-01

This work is concerned with the application of atomistic field theory (AFT) in modeling and simulation of polarizable materials under an electromagnetic (EM) field. AFT enables us to express an atomic scale local property of a multi-element crystalline (which has more than one kind of atom in the unit cell) system in terms of the distortions of lattice cells and the rearrangement of atoms within the lattice cell, thereby making AFT suitable to fully reproduce both acoustic and optical branches in phonon dispersion relations. Due to the applied EM field, the inhomogeneous motions of discrete atoms in the polarizable crystal give rise to the rearrangement of microstructure and polarization. The AFT and its corresponding finite element implementation are briefly introduced. Single-crystal MgO nanowires under an EM field is modeled and simulated. The numerical results have demonstrated that AFT can serve as a tool to analyze the electromagnetic phenomena of multi-element crystal materials at micro/nano-level within a field framework

Atomistic simulation of CO 2 solubility in poly(ethylene oxide) oligomers

KAUST Repository

Hong, Bingbing; Panagiotopoulos, Athanassios Z.

2013-01-01

We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

Directory of Open Access Journals (Sweden)

Pavel V. Komarov

2013-09-01

Full Text Available Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic and minority (hydrophilic subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping mechanism as a significant contributor to the proton conductivity.

Passing waves from atomistic to continuum

Science.gov (United States)

Chen, Xiang; Diaz, Adrian; Xiong, Liming; McDowell, David L.; Chen, Youping

2018-02-01

Progress in the development of coupled atomistic-continuum methods for simulations of critical dynamic material behavior has been hampered by a spurious wave reflection problem at the atomistic-continuum interface. This problem is mainly caused by the difference in material descriptions between the atomistic and continuum models, which results in a mismatch in phonon dispersion relations. In this work, we introduce a new method based on atomistic dynamics of lattice coupled with a concurrent atomistic-continuum method to enable a full phonon representation in the continuum description. This permits the passage of short-wavelength, high-frequency phonon waves from the atomistic to continuum regions. The benchmark examples presented in this work demonstrate that the new scheme enables the passage of all allowable phonons through the atomistic-continuum interface; it also preserves the wave coherency and energy conservation after phonons transport across multiple atomistic-continuum interfaces. This work is the first step towards developing a concurrent atomistic-continuum simulation tool for non-equilibrium phonon-mediated thermal transport in materials with microstructural complexity.

Spatiotemporal exploratory models for broad-scale survey data.

Science.gov (United States)

Fink, Daniel; Hochachka, Wesley M; Zuckerberg, Benjamin; Winkler, David W; Shaby, Ben; Munson, M Arthur; Hooker, Giles; Riedewald, Mirek; Sheldon, Daniel; Kelling, Steve

2010-12-01

The distributions of animal populations change and evolve through time. Migratory species exploit different habitats at different times of the year. Biotic and abiotic features that determine where a species lives vary due to natural and anthropogenic factors. This spatiotemporal variation needs to be accounted for in any modeling of species' distributions. In this paper we introduce a semiparametric model that provides a flexible framework for analyzing dynamic patterns of species occurrence and abundance from broad-scale survey data. The spatiotemporal exploratory model (STEM) adds essential spatiotemporal structure to existing techniques for developing species distribution models through a simple parametric structure without requiring a detailed understanding of the underlying dynamic processes. STEMs use a multi-scale strategy to differentiate between local and global-scale spatiotemporal structure. A user-specified species distribution model accounts for spatial and temporal patterning at the local level. These local patterns are then allowed to "scale up" via ensemble averaging to larger scales. This makes STEMs especially well suited for exploring distributional dynamics arising from a variety of processes. Using data from eBird, an online citizen science bird-monitoring project, we demonstrate that monthly changes in distribution of a migratory species, the Tree Swallow (Tachycineta bicolor), can be more accurately described with a STEM than a conventional bagged decision tree model in which spatiotemporal structure has not been imposed. We also demonstrate that there is no loss of model predictive power when a STEM is used to describe a spatiotemporal distribution with very little spatiotemporal variation; the distribution of a nonmigratory species, the Northern Cardinal (Cardinalis cardinalis).

Dynamic aspects of dislocation motion: atomistic simulations

International Nuclear Information System (INIS)

Bitzek, Erik; Gumbsch, Peter

2005-01-01

Atomistic simulations of accelerating edge and screw dislocations were carried out to study the dynamics of dislocations in a face centered cubic metal. Using two different embedded atom potentials for nickel and a simple slab geometry, the Peierls stress, the effective mass, the line tension and the drag coefficient were determined. A dislocation intersecting an array of voids is used to study dynamic effects in dislocation-obstacle interactions. A pronounced effect caused by inertial overshooting is found. A dynamic line tension model is developed which reproduces the simulation results. The model can be used to easily estimate the magnitude of inertial effects in the interaction of dislocations with localized obstacles for different obstacle strengths, -spacings and temperatures

Solid solution hardening in face centered binary alloys: Gliding statistics of a dislocation in random solid solution by atomistic simulation

International Nuclear Information System (INIS)

Patinet, S.

2009-12-01

The glide of edge and screw dislocation in solid solution is modeled through atomistic simulations in two model alloys of Ni(Al) and Al(Mg) described within the embedded atom method. Our approach is based on the study of the elementary interaction between dislocations and solutes to derive solid solution hardening of face centered cubic binary alloys. We identify the physical origins of the intensity and range of the interaction between a dislocation and a solute atom. The thermally activated crossing of a solute atom by a dislocation is studied at the atomistic scale. We show that hardening of edge and screw segments are similar. We develop a line tension model that reproduces quantitatively the atomistic calculations of the flow stress. We identify the universality class to which the dislocation depinning transition in solid solution belongs. (author)

Shape evolution of nanostructures by thermal and ion beam processing. Modeling and atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Roentzsch, L.

2007-07-01

Single-crystalline nanostructures often exhibit gradients of surface (and/or interface) curvature that emerge from fabrication and growth processes or from thermal fluctuations. Thus, the system-inherent capillary force can initiate morphological transformations during further processing steps or during operation at elevated temperature. Therefore and because of the ongoing miniaturization of functional structures which causes a general rise in surface-to-volume ratios, solid-state capillary phenomena will become increasingly important: On the one hand diffusion-mediated capillary processes can be of practical use in view of non-conventional nanostructure fabrication methods based on self-organization mechanisms, on the other hand they can destroy the integrity of nanostructures which can go along with the failure of functionality. Additionally, capillarity-induced shape transformations are effected and can thereby be controlled by applied fields and forces (guided or driven evolution). With these prospects and challenges at hand, formation and shape transformation of single-crystalline nanostructures due to the system-inherent capillary force in combination with external fields or forces are investigated in the frame of this dissertation by means of atomistic computer simulations. For the exploration (search, description, and prediction) of reaction pathways of nanostructure shape transformations, kinetic Monte Carlo (KMC) simulations are the method of choice. Since the employed KMC code is founded on a cellular automaton principle, the spatio-temporal development of lattice-based N-particle systems (N up to several million) can be followed for time spans of several orders of magnitude, while considering local phenomena due to atomic-scale effects like diffusion, nucleation, dissociation, or ballistic displacements. In this work, the main emphasis is put on nanostructures which have a cylindrical geometry, for example, nanowires (NWs), nanorods, nanotubes etc

Shape evolution of nanostructures by thermal and ion beam processing. Modeling and atomistic simulations

International Nuclear Information System (INIS)

Roentzsch, L.

2007-01-01

Single-crystalline nanostructures often exhibit gradients of surface (and/or interface) curvature that emerge from fabrication and growth processes or from thermal fluctuations. Thus, the system-inherent capillary force can initiate morphological transformations during further processing steps or during operation at elevated temperature. Therefore and because of the ongoing miniaturization of functional structures which causes a general rise in surface-to-volume ratios, solid-state capillary phenomena will become increasingly important: On the one hand diffusion-mediated capillary processes can be of practical use in view of non-conventional nanostructure fabrication methods based on self-organization mechanisms, on the other hand they can destroy the integrity of nanostructures which can go along with the failure of functionality. Additionally, capillarity-induced shape transformations are effected and can thereby be controlled by applied fields and forces (guided or driven evolution). With these prospects and challenges at hand, formation and shape transformation of single-crystalline nanostructures due to the system-inherent capillary force in combination with external fields or forces are investigated in the frame of this dissertation by means of atomistic computer simulations. For the exploration (search, description, and prediction) of reaction pathways of nanostructure shape transformations, kinetic Monte Carlo (KMC) simulations are the method of choice. Since the employed KMC code is founded on a cellular automaton principle, the spatio-temporal development of lattice-based N-particle systems (N up to several million) can be followed for time spans of several orders of magnitude, while considering local phenomena due to atomic-scale effects like diffusion, nucleation, dissociation, or ballistic displacements. In this work, the main emphasis is put on nanostructures which have a cylindrical geometry, for example, nanowires (NWs), nanorods, nanotubes etc

Spatio-temporal scaling of channels in braided streams.

Science.gov (United States)

A.G. Hunt; G.E. Grant; V.K. Gupta

2006-01-01

The spatio-temporal scaling relationship for individual channels in braided streams is shown to be identical to the spatio-temporal scaling associated with constant Froude number, e.g., Fr = l. A means to derive this relationship is developed from a new theory of sediment transport. The mechanism by which the Fr = l condition apparently governs the scaling seems to...

Multiscale modeling of dislocation processes in BCC tantalum: bridging atomistic and mesoscale simulations

International Nuclear Information System (INIS)

Yang, L H; Tang, M; Moriarty, J A

2001-01-01

Plastic deformation in bcc metals at low temperatures and high-strain rates is controlled by the motion of a/2 screw dislocations, and understanding the fundamental atomistic processes of this motion is essential to develop predictive multiscale models of crystal plasticity. The multiscale modeling approach presented here for bcc Ta is based on information passing, where results of simulations at the atomic scale are used in simulations of plastic deformation at mesoscopic length scales via dislocation dynamics (DD). The relevant core properties of a/2 screw dislocations in Ta have been obtained using quantum-based interatomic potentials derived from model generalized pseudopotential theory and an ab-initio data base together with an accurate Green's-function simulation method that implements flexible boundary conditions. In particular, the stress-dependent activation enthalpy for the lowest-energy kink-pair mechanism has been calculated and fitted to a revealing analytic form. This is the critical quantity determining dislocation mobility in the DD simulations, and the present activation enthalpy is found to be in good agreement with the previous empirical form used to explain the temperature dependence of the yield stress

Atomistic simulation studies of iron sulphide, platinum antimonide and platinum arsenide

CSIR Research Space (South Africa)

Ngoepe, PE

2005-09-01

Full Text Available The authors present the results of atomistic simulations using derived interatomic potentials for the pyrite-structured metal chalcogenides FeS2, PtSb2 and PtAs2. Structural and elastic constants were calculated and compared with experimental...

Adaptive resolution simulation of an atomistic protein in MARTINI water

International Nuclear Information System (INIS)

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej

2014-01-01

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations

Using a weather generator to downscale spatio-temporal precipitation at urban scale

DEFF Research Database (Denmark)

Sørup, Hjalte Jomo Danielsen; Christensen, Ole Bøssing; Arnbjerg-Nielsen, Karsten

In recent years, urban flooding has occurred in Denmark due to very local extreme precipitation events with very short lifetime. Several of these floods have been among the most severe ever experienced. The current study demonstrates the applicability of the Spatio-Temporal Neyman-Scott Rectangular...... the observed spatio-temporal differences at very fine scale for all measured parameters. For downscaling, perturbation with a climate change signal, precipitation from four different regional climate model simulations has been analysed. The analysed models are two runs from the ENSEMBLES (RACMO...

Atomistic computer simulations of FePt nanoparticles. Thermodynamic and kinetic properties

Energy Technology Data Exchange (ETDEWEB)

Mueller, M.

2007-12-20

In the present dissertation, a hierarchical multiscale approach for modeling FePt nanoparticles by atomistic computer simulations is developed. By describing the interatomic interactions on different levels of sophistication, various time and length scales can be accessed. Methods range from static quantum-mechanic total-energy calculations of small periodic systems to simulations of whole particles over an extended time by using simple lattice Hamiltonians. By employing these methods, the energetic and thermodynamic stability of non-crystalline multiply twinned FePt nanoparticles is investigated. Subsequently, the thermodynamics of the order-disorder transition in FePt nanoparticles is analyzed, including the influence of particle size, composition and modified surface energies by different chemical surroundings. In order to identify processes that reduce or enhance the rate of transformation from the disordered to the ordered state, the kinetics of the ordering transition in FePt nanoparticles is finally investigated by assessing the contributions of surface and volume diffusion. (orig.)

Fatigue mechanisms in an austenitic steel under cyclic loading: Experiments and atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Soppa, E.A., E-mail: ewa.soppa@mpa.uni-stuttgart.de; Kohler, C., E-mail: christopher.kohler@mpa.uni-stuttgart.de; Roos, E., E-mail: eberhard.roos@mpa.uni-stuttgart.de

2014-03-01

Experimental investigations on the austenitic stainless steel X6CrNiNb18-10 (AISI – 347) and concomitant atomistic simulations of a FeNi nanocrystalline model system have been performed in order to understand the basic mechanisms of fatigue damage under cyclic loading. Using electron backscatter diffraction (EBSD) the influence of deformation induced martensitic transformation and NbC size distribution on the fatigue crack formation has been demonstrated. The martensite nucleates prevalently at grain boundaries, triple points and at the specimen free surface and forms small (∼1 µm sized) differently oriented grains. The atomistic simulations show the role of regions of a high density of stacking faults for the martensitic transformation.

Fermi-level effects in semiconductor processing: A modeling scheme for atomistic kinetic Monte Carlo simulators

Science.gov (United States)

Martin-Bragado, I.; Castrillo, P.; Jaraiz, M.; Pinacho, R.; Rubio, J. E.; Barbolla, J.; Moroz, V.

2005-09-01

Atomistic process simulation is expected to play an important role for the development of next generations of integrated circuits. This work describes an approach for modeling electric charge effects in a three-dimensional atomistic kinetic Monte Carlo process simulator. The proposed model has been applied to the diffusion of electrically active boron and arsenic atoms in silicon. Several key aspects of the underlying physical mechanisms are discussed: (i) the use of the local Debye length to smooth out the atomistic point-charge distribution, (ii) algorithms to correctly update the charge state in a physically accurate and computationally efficient way, and (iii) an efficient implementation of the drift of charged particles in an electric field. High-concentration effects such as band-gap narrowing and degenerate statistics are also taken into account. The efficiency, accuracy, and relevance of the model are discussed.

Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design

International Nuclear Information System (INIS)

Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.

2010-01-01

atomistic simulations, e.g., molecular dynamics and density functional theory (DFT). The latter two atomistic techniques are handicapped by the onerous length and time scales associated with simulating mesoscopic materials. Simulating such mesoscopic materials is likely to require, and greatly benefit from multiscale simulations coupling DFT, MD, PD, and explicit transient dynamic finite element methods FEM (e.g., Presto). The proposed work fills the gap needed to enable multiscale materials simulations.

Atomistically-informed dislocation dynamics in FCC crystals

International Nuclear Information System (INIS)

Martinez, E.; Marian, J.; Arsenlis, A.; Victoria, M.; Martinez, E.; Victoria, M.; Perlado, J.M.

2008-01-01

Full text of publication follows. We will present a nodal dislocation dynamics (DD) model to simulate plastic processes in fcc crystals. The model explicitly accounts for all slip systems and Burgers vectors observed in fcc systems, including stacking faults and partial dislocations. We derive simple conservation rules that describe all partial dislocation interactions rigorously and allow us to model and quantify cross-slip processes, the structure and strength of dislocation junctions, and the formation of fcc-specific structures such as stacking fault tetrahedra. The DD framework is built upon isotropic non-singular linear elasticity, and supports itself on information transmitted from the atomistic scale. In this fashion, connection between the meso and micro scales is attained self-consistently with core parameters fitted to atomistic data. We perform a series of targeted simulations to demonstrate the capabilities of the model, including dislocation reactions and dissociations and dislocation junction strength. Additionally we map the four-dimensional stress space relevant for cross-slip and relate our fundings to the plastic behaviour of' monocrystalline fcc metals. (authors)

Atomistic simulation and continuum modeling of graphene nanoribbons under uniaxial tension

International Nuclear Information System (INIS)

Lu, Qiang; Gao, Wei; Huang, Rui

2011-01-01

Atomistic simulations are performed to study the nonlinear mechanical behavior of graphene nanoribbons under quasistatic uniaxial tension, emphasizing the effects of edge structures (armchair and zigzag, without and with hydrogen passivation) on elastic modulus and fracture strength. The numerical results are analyzed within a theoretical model of thermodynamics, which enables determination of the bulk strain energy density, the edge energy density and the hydrogen adsorption energy density as nonlinear functions of the applied strain based on static molecular mechanics simulations. These functions can be used to describe mechanical behavior of graphene nanoribbons from the initial linear elasticity to fracture. It is found that the initial Young's modulus of a graphene nanoribbon depends on the ribbon width and the edge chirality. Furthermore, it is found that the nominal strain to fracture is considerably lower for graphene nanoribbons with armchair edges than for ribbons with zigzag edges. Molecular dynamics simulations reveal two distinct fracture nucleation mechanisms: homogeneous nucleation for the zigzag-edged graphene nanoribbons and edge-controlled heterogeneous nucleation for the armchair-edged ribbons. The modeling and simulations in this study highlight the atomistic mechanisms for the nonlinear mechanical behavior of graphene nanoribbons with the edge effects, which is potentially important for developing integrated graphene-based devices

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

Science.gov (United States)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

Development of porous structure simulator for multi-scale simulation of irregular porous catalysts

International Nuclear Information System (INIS)

Koyama, Michihisa; Suzuki, Ai; Sahnoun, Riadh; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A.; Miyamoto, Akira

2008-01-01

Efficient development of highly functional porous materials, used as catalysts in the automobile industry, demands a meticulous knowledge of the nano-scale interface at the electronic and atomistic scale. However, it is often difficult to correlate the microscopic interfacial interactions with macroscopic characteristics of the materials; for instance, the interaction between a precious metal and its support oxide with long-term sintering properties of the catalyst. Multi-scale computational chemistry approaches can contribute to bridge the gap between micro- and macroscopic characteristics of these materials; however this type of multi-scale simulations has been difficult to apply especially to porous materials. To overcome this problem, we have developed a novel mesoscopic approach based on a porous structure simulator. This simulator can construct automatically irregular porous structures on a computer, enabling simulations with complex meso-scale structures. Moreover, in this work we have developed a new method to simulate long-term sintering properties of metal particles on porous catalysts. Finally, we have applied the method to the simulation of sintering properties of Pt on alumina support. This newly developed method has enabled us to propose a multi-scale simulation approach for porous catalysts

Atomistic Simulation of the Rate-Dependent Ductile-to-Brittle Failure Transition in Bicrystalline Metal Nanowires.

Science.gov (United States)

Tao, Weiwei; Cao, Penghui; Park, Harold S

2018-02-14

The mechanical properties and plastic deformation mechanisms of metal nanowires have been studied intensely for many years. One of the important yet unresolved challenges in this field is to bridge the gap in properties and deformation mechanisms reported for slow strain rate experiments (∼10 -2 s -1 ), and high strain rate molecular dynamics (MD) simulations (∼10 8 s -1 ) such that a complete understanding of strain rate effects on mechanical deformation and plasticity can be obtained. In this work, we use long time scale atomistic modeling based on potential energy surface exploration to elucidate the atomistic mechanisms governing a strain-rate-dependent incipient plasticity and yielding transition for face centered cubic (FCC) copper and silver nanowires. The transition occurs for both metals with both pristine and rough surfaces for all computationally accessible diameters (ductile-to-brittle transition in failure mode similar to previous experimental studies on bicrystalline silver nanowires is observed, which is driven by differences in dislocation activity and grain boundary mobility as compared to the high strain rate case.

Robust mode space approach for atomistic modeling of realistically large nanowire transistors

Science.gov (United States)

Huang, Jun Z.; Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard

2018-01-01

Nanoelectronic transistors have reached 3D length scales in which the number of atoms is countable. Truly atomistic device representations are needed to capture the essential functionalities of the devices. Atomistic quantum transport simulations of realistically extended devices are, however, computationally very demanding. The widely used mode space (MS) approach can significantly reduce the numerical cost, but a good MS basis is usually very hard to obtain for atomistic full-band models. In this work, a robust and parallel algorithm is developed to optimize the MS basis for atomistic nanowires. This enables engineering-level, reliable tight binding non-equilibrium Green's function simulation of nanowire metal-oxide-semiconductor field-effect transistor (MOSFET) with a realistic cross section of 10 nm × 10 nm using a small computer cluster. This approach is applied to compare the performance of InGaAs and Si nanowire n-type MOSFETs (nMOSFETs) with various channel lengths and cross sections. Simulation results with full-band accuracy indicate that InGaAs nanowire nMOSFETs have no drive current advantage over their Si counterparts for cross sections up to about 10 nm × 10 nm.

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

Science.gov (United States)

Rapaport, D C

2009-04-01

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

Science.gov (United States)

Zhang, Zhiwei; Chen, Pei; Qin, Fei; An, Tong; Yu, Huiping

2018-05-01

Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD) layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young's modulus, ultimate tensile strength (UTS), and strain at fracture is observed.

Mechanical properties of silicon in subsurface damage layer from nano-grinding studied by atomistic simulation

Directory of Open Access Journals (Sweden)

Zhiwei Zhang

2018-05-01

Full Text Available Ultra-thin silicon wafer is highly demanded by semi-conductor industry. During wafer thinning process, the grinding technology will inevitably induce damage to the surface and subsurface of silicon wafer. To understand the mechanism of subsurface damage (SSD layer formation and mechanical properties of SSD layer, atomistic simulation is the effective tool to perform the study, since the SSD layer is in the scale of nanometer and hardly to be separated from underneath undamaged silicon. This paper is devoted to understand the formation of SSD layer, and the difference between mechanical properties of damaged silicon in SSD layer and ideal silicon. With the atomistic model, the nano-grinding process could be performed between a silicon workpiece and diamond tool under different grinding speed. To reach a thinnest SSD layer, nano-grinding speed will be optimized in the range of 50-400 m/s. Mechanical properties of six damaged silicon workpieces with different depths of cut will be studied. The SSD layer from each workpiece will be isolated, and a quasi-static tensile test is simulated to perform on the isolated SSD layer. The obtained stress-strain curve is an illustration of overall mechanical properties of SSD layer. By comparing the stress-strain curves of damaged silicon and ideal silicon, a degradation of Young’s modulus, ultimate tensile strength (UTS, and strain at fracture is observed.

Atomistic simulation of graphene-based polymer nanocomposites

International Nuclear Information System (INIS)

Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

2016-01-01

Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

Dynamic characteristics of nanoindentation using atomistic simulation

International Nuclear Information System (INIS)

Fang, Te-Hua; Chang, Wen-Yang; Huang, Jian-Jin

2009-01-01

Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0 o , is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

Dynamic characteristics of nanoindentation using atomistic simulation

Energy Technology Data Exchange (ETDEWEB)

Fang, Te-Hua, E-mail: fang.tehua@msa.hinet.net [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China); Chang, Wen-Yang [Microsystems Technology Center, Industrial Technology Research Institute, Tainan 709, Taiwan (China); Huang, Jian-Jin [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China)

2009-06-15

Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0{sup o}, is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

Atomic scale simulations for improved CRUD and fuel performance modeling

Energy Technology Data Exchange (ETDEWEB)

Andersson, Anders David Ragnar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cooper, Michael William Donald [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-01-06

A more mechanistic description of fuel performance codes can be achieved by deriving models and parameters from atomistic scale simulations rather than fitting models empirically to experimental data. The same argument applies to modeling deposition of corrosion products on fuel rods (CRUD). Here are some results from publications in 2016 carried out using the CASL allocation at LANL.

Atomistic to Continuum Multiscale and Multiphysics Simulation of NiTi Shape Memory Alloy

Science.gov (United States)

Gur, Sourav

Shape memory alloys (SMAs) are materials that show reversible, thermo-elastic, diffusionless, displacive (solid to solid) phase transformation, due to the application of temperature and/ or stress (/strain). Among different SMAs, NiTi is a popular one. NiTi shows reversible phase transformation, the shape memory effect (SME), where irreversible deformations are recovered upon heating, and superelasticity (SE), where large strains imposed at high enough temperatures are fully recovered. Phase transformation process in NiTi SMA is a very complex process that involves the competition between developed internal strain and phonon dispersion instability. In NiTi SMA, phase transformation occurs over a wide range of temperature and/ or stress (strain) which involves, evolution of different crystalline phases (cubic austenite i.e. B2, different monoclinic variant of martensite i.e. B19', and orthorhombic B19 or BCO structures). Further, it is observed from experimental and computational studies that the evolution kinetics and growth rate of different phases in NiTi SMA vary significantly over a wide spectrum of spatio-temporal scales, especially with length scales. At nano-meter length scale, phase transformation temperatures, critical transformation stress (or strain) and phase fraction evolution change significantly with sample or simulation cell size and grain size. Even, below a critical length scale, the phase transformation process stops. All these aspects make NiTi SMA very interesting to the science and engineering research community and in this context, the present focuses on the following aspects. At first this study address the stability, evolution and growth kinetics of different phases (B2 and variants of B19'), at different length scales, starting from the atomic level and ending at the continuum macroscopic level. The effects of simulation cell size, grain size, and presence of free surface and grain boundary on the phase transformation process

Atomistic simulations of surfactant adsorption kinetics at interfaces

Science.gov (United States)

Iskrenova, Eugeniya; Patnaik, Soumya

2014-03-01

Heat transfer control and enhancement is an important and challenging problem in a variety of industrial and technological applications including aircraft thermal management. The role of additives in nucleate boiling and phase change in general has long been recognized and studied experimentally and modeled theoretically but in-depth description and atomistic understanding of the multiscale processes involved are still needed for better prediction and control of the heat transfer efficiency. Surfactant additives have been experimentally observed to either enhance or inhibit the boiling heat transfer depending on the surfactant concentration and chemistry and, on a molecular level, their addition leads to dynamic surface tension and changes in interfacial and transfer properties, thus contributing to the complexity of the problem. We present our atomistic modeling study of the interfacial adsorption kinetics of aqueous surfactant (sodium dodecyl sulfate) systems at a range of concentrations at room and boiling temperatures. Classical molecular dynamics and Umbrella Sampling simulations were used to study the surfactant transport properties and estimate the adsorption and desorption rates at liquid-vacuum and liquid-solid interfaces. The authors gratefully acknowledge funding from AFOSR Thermal Science Program and the Air Force Research Laboratory DoD Supercomputing Resource Center for computing time and resources.

3d visualization of atomistic simulations on every desktop

Science.gov (United States)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-08-01

Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

3d visualization of atomistic simulations on every desktop

International Nuclear Information System (INIS)

Peled, Dan; Silverman, Amihai; Adler, Joan

2013-01-01

Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given

Control of density fluctuations in atomistic-continuum simulations of dense liquids

DEFF Research Database (Denmark)

Kotsalis, E.M.; Walther, Jens Honore; Koumoutsakos, P.

2007-01-01

with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force...... is usually employed to remedy this situation.We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity...

De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers

Energy Technology Data Exchange (ETDEWEB)

Nakano, A; Kalia, R K; Nomura, K; Sharma, A; Vashishta, P; Shimojo, F; van Duin, A; Goddard, III, W A; Biswas, R; Srivastava, D; Yang, L H

2006-09-04

We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and geographically distributed clusters. In this framework, high-end chemically reactive and non-reactive molecular dynamics (MD) simulations explore a wide solution space to discover microscopic mechanisms that govern macroscopic material properties, into which highly accurate quantum mechanical (QM) simulations are embedded to validate the discovered mechanisms and quantify the uncertainty of the solution. The framework includes an embedded divide-and-conquer (EDC) algorithmic framework for the design of linear-scaling simulation algorithms with minimal bandwidth complexity and tight error control. The EDC framework also enables adaptive hierarchical simulation with automated model transitioning assisted by graph-based event tracking. A tunable hierarchical cellular decomposition parallelization framework then maps the O(N) EDC algorithms onto Petaflops computers, while achieving performance tunability through a hierarchy of parameterized cell data/computation structures, as well as its implementation using hybrid Grid remote procedure call + message passing + threads programming. High-end computing platforms such as IBM BlueGene/L, SGI Altix 3000 and the NSF TeraGrid provide an excellent test grounds for the framework. On these platforms, we have achieved unprecedented scales of quantum-mechanically accurate and well validated, chemically reactive atomistic simulations--1.06 billion-atom fast reactive force-field MD and 11.8 million-atom (1.04 trillion grid points) quantum-mechanical MD in the framework of the EDC density functional theory on adaptive multigrids--in addition to 134 billion-atom non-reactive space-time multiresolution MD, with the parallel efficiency as high as 0.998 on 65,536 dual-processor BlueGene/L nodes. We have also achieved an automated execution of hierarchical QM

An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

Energy Technology Data Exchange (ETDEWEB)

Wang, Zhi [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Jiang, Xiang-Wei; Li, Shu-Shen [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Wang, Lin-Wang, E-mail: lwwang@lbl.gov [Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

2014-03-24

We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10{sup 5} atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose.

An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

International Nuclear Information System (INIS)

Wang, Zhi; Jiang, Xiang-Wei; Li, Shu-Shen; Wang, Lin-Wang

2014-01-01

We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10 5 atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose

A continuum-atomistic simulation of heat transfer in micro- and nano-flows

International Nuclear Information System (INIS)

Liu Jin; Chen Shiyi; Nie Xiaobo; Robbins, Mark O.

2007-01-01

We develop a hybrid atomistic-continuum scheme for simulating micro- and nano-flows with heat transfer. The approach is based on spatial 'domain decomposition' in which molecular dynamics (MD) is used in regions where atomistic details are important, while classical continuum fluid dynamics is used in the remaining regions. The two descriptions are matched in a coupling region where we ensure continuity of mass, momentum, energy and their fluxes. The scheme for including the energy equation is implemented in 1-D and 2-D, and used to study steady and unsteady heat transfer in channel flows with and without nano roughness. Good agreement between hybrid results and analytical or pure MD results is found, demonstrating the accuracy of this multiscale method and its potential applications in thermal engineering

Simulating Surface-Enhanced Hyper-Raman Scattering Using Atomistic Electrodynamics-Quantum Mechanical Models.

Science.gov (United States)

Hu, Zhongwei; Chulhai, Dhabih V; Jensen, Lasse

2016-12-13

Surface-enhanced hyper-Raman scattering (SEHRS) is the two-photon analogue of surface-enhanced Raman scattering (SERS), which has proven to be a powerful tool to study molecular structures and surface enhancements. However, few theoretical approaches to SEHRS exist and most neglect the atomistic descriptions of the metal surface and molecular resonance effects. In this work, we present two atomistic electrodynamics-quantum mechanical models to simulate SEHRS. The first is the discrete interaction model/quantum mechanical (DIM/QM) model, which combines an atomistic electrodynamics model of the nanoparticle with a time-dependent density functional theory description of the molecule. The second model is a dressed-tensors method that describes the molecule as a point-dipole and point-quadrupole object interacting with the enhanced local field and field-gradients (FG) from the nanoparticle. In both of these models, the resonance effects are treated efficiently by means of damped quadratic response theory. Using these methods, we simulate SEHRS spectra for benzene and pyridine. Our results show that the FG effects in SEHRS play an important role in determining both the surface selection rules and the enhancements. We find that FG effects are more important in SEHRS than in SERS. We also show that the spectral features of small molecules can be accurately described by accounting for the interactions between the molecule and the local field and FG of the nanoparticle. However, at short distances between the metal and molecule, we find significant differences in the SEHRS enhancements predicted using the DIM/QM and the dressed-tensors methods.

From HADES to PARADISE-atomistic simulation of defects in minerals

Energy Technology Data Exchange (ETDEWEB)

Parker, Stephen C; Cooke, David J; Kerisit, Sebastien; Marmier, Arnaud S; Taylor, Sarah L; Taylor, Stuart N [Department of Chemistry, University of Bath, Bath BA2 7AY (United Kingdom)

2004-07-14

The development of the HADES code by Michael Norgett in the 1970s enabled, for the first time, the routine simulation of point defects in inorganic solids at the atomic scale. Using examples from current research we illustrate how the scope and applications of atomistic simulations have widened with time and yet still follow an approach readily identifiable with this early work. Firstly we discuss the use of the Mott-Littleton methodology to study the segregation of various isovalent cations to the (00.1) and (01.2) surfaces of haematite ({alpha}-Fe{sub 2}O{sub 3}). The results show that the size of the impurities has a considerable effect on the magnitude of the segregation energy. We then extend these simulations to investigate the effect of the concentration of the impurities at the surface on the segregation process using a supercell approach. We consider next the effect of segregation to stepped surfaces illustrating this with recent work on segregation of La{sup 3+} to CaF{sub 2} surfaces, which show enhanced segregation to step edges. We discuss next the application of lattice dynamics to modelling point defects in complex oxide materials by applying this to the study of hydrogen incorporation into {beta}-Mg{sub 2}SiO{sub 4}. Finally our attention is turned to a method for considering the surface energy of physically defective surfaces and we illustrate its approach by considering the low index surfaces of {alpha}-Al{sub 2}O{sub 3}.

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

DEFF Research Database (Denmark)

Euro, Liliya; Haapanen, Outi; Róg, Tomasz

2017-01-01

of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

Molecular Dynamics Simulations for Resolving Scaling Laws of Polyethylene Melts

Directory of Open Access Journals (Sweden)

Kazuaki Z. Takahashi

2017-01-01

Full Text Available Long-timescale molecular dynamics simulations were performed to estimate the actual physical nature of a united-atom model of polyethylene (PE. Several scaling laws for representative polymer properties are compared to theoretical predictions. Internal structure results indicate a clear departure from theoretical predictions that assume ideal chain statics. Chain motion deviates from predictions that assume ideal motion of short chains. With regard to linear viscoelasticity, the presence or absence of entanglements strongly affects the duration of the theoretical behavior. Overall, the results indicate that Gaussian statics and dynamics are not necessarily established for real atomistic models of PE. Moreover, the actual physical nature should be carefully considered when using atomistic models for applications that expect typical polymer behaviors.

Collaborative simulation method with spatiotemporal synchronization process control

Science.gov (United States)

Zou, Yisheng; Ding, Guofu; Zhang, Weihua; Zhang, Jian; Qin, Shengfeng; Tan, John Kian

2016-10-01

When designing a complex mechatronics system, such as high speed trains, it is relatively difficult to effectively simulate the entire system's dynamic behaviors because it involves multi-disciplinary subsystems. Currently,a most practical approach for multi-disciplinary simulation is interface based coupling simulation method, but it faces a twofold challenge: spatial and time unsynchronizations among multi-directional coupling simulation of subsystems. A new collaborative simulation method with spatiotemporal synchronization process control is proposed for coupling simulating a given complex mechatronics system across multiple subsystems on different platforms. The method consists of 1) a coupler-based coupling mechanisms to define the interfacing and interaction mechanisms among subsystems, and 2) a simulation process control algorithm to realize the coupling simulation in a spatiotemporal synchronized manner. The test results from a case study show that the proposed method 1) can certainly be used to simulate the sub-systems interactions under different simulation conditions in an engineering system, and 2) effectively supports multi-directional coupling simulation among multi-disciplinary subsystems. This method has been successfully applied in China high speed train design and development processes, demonstrating that it can be applied in a wide range of engineering systems design and simulation with improved efficiency and effectiveness.

Spatiotemporal Scaling Effect on Rainfall Network Design Using Entropy

Directory of Open Access Journals (Sweden)

Chiang Wei

2014-08-01

Full Text Available Because of high variation in mountainous areas, rainfall data at different spatiotemporal scales may yield potential uncertainty for network design. However, few studies focus on the scaling effect on both the spatial and the temporal scale. By calculating the maximum joint entropy of hourly typhoon events, monthly, six dry and wet months and annual rainfall between 1992 and 2012 for 1-, 3-, and 5-km grids, the relocated candidate rain gauges in the National Taiwan University Experimental Forest of Central Taiwan are prioritized. The results show: (1 the network exhibits different locations for first prioritized candidate rain gauges for different spatiotemporal scales; (2 the effect of spatial scales is insignificant compared to temporal scales; and (3 a smaller number and a lower percentage of required stations (PRS reach stable joint entropy for a long duration at finer spatial scale. Prioritized candidate rain gauges provide key reference points for adjusting the network to capture more accurate information and minimize redundancy.

Atomistic simulations of dislocation-precipitate interactions emphasize importance of cross-slip

International Nuclear Information System (INIS)

Singh, C.V.; Mateos, A.J.; Warner, D.H.

2011-01-01

This work examines the interaction of screw dislocations with Guinier-Preston (GP) zones using atomistic simulations. Both Orowan looping and cross-slip mechanisms are found to control the interactions. Cross-slip, occurring both at zero and finite temperatures, is found to either significantly reduce or enhance precipitate strengthening, depending upon the orientation of the dislocation-GP zone interaction. The orientation dependence, and its dependence on temperature, provides a micromechanical explanation for the experiments of Muraishi et al. (Philos. Mag. A 82 (2002) 2755).

Structural and functional analysis of glycoprotein butyrylcholinesterase using atomistic molecular dynamics

Science.gov (United States)

Bernardi, Austen; Faller, Roland

Atomistic molecular dynamics (MD) has proven to be a powerful tool for studying the structure and dynamics of biological systems on nanosecond to microsecond time scales and nanometer length scales. In this work we study the effects of modifying the glycan distribution on the structure and function of full length monomeric butyrylcholinesterase (BChE). BChE exists as a monomer, dimer, or tetramer, and is a therapeutic glycoprotein with nine asparagine glycosylation sites per monomer. Each monomer acts as a stoichiometric scavenger for organophosphorus (OP) nerve agents (e.g. sarin, soman). Glycan distributions are highly heterogeneous and have been shown experimentally to affect certain glycoproteins' stability and reactivity. We performed structural analysis of various biologically relevant glycoforms of BChE using classical atomistic MD. Functional analysis was performed through binding energy simulations using umbrella sampling with BChE and OP cofactors. Additionally, we assess the quality of the glycans' conformational sampling. We found that the glycan distribution has a significant effect on the structure and function of BChE on timescales available to atomistic MD. This project is funded by the DTRA Grant HDTRA1-15-1-0054.

A coupled atomistics and discrete dislocation plasticity simulation of nanoindentation into single crystal thin films

International Nuclear Information System (INIS)

Miller, Ronald E.; Shilkrot, L.E.; Curtin, William A.

2004-01-01

The phenomenon of 2D nanoindentation of circular 'Brinell' indenter into a single crystal metal thin film bonded to a rigid substrate is investigated. The simulation method is the coupled atomistics and discrete dislocation (CADD) model recently developed by the authors. The CADD model couples a continuum region containing any number of discrete dislocations to an atomistic region, and permits accurate, automatic detection and passing of dislocations between the atomistic and continuum regions. The CADD model allows for a detailed study of nanoindentation to large penetration depths (up to 60 A here) using only a small region of atoms just underneath the indenter where dislocation nucleation, cross-slip, and annihilation occur. Indentation of a model hexagonal aluminum crystal shows: (i) the onset of homogeneous dislocation nucleation at points away from the points of maximum resolved shear stress; (ii) size-dependence of the material hardness, (iii) the role of dislocation dissociation on deformation; (iv) reverse plasticity, including nucleation of dislocations on unloading and annihilation; (v) permanent deformation, including surface uplift, after full unloading; (vi) the effects of film thickness on the load-displacement response; and (vii) the differences between displacement and force controlled loading. This application demonstrates the power of the CADD method in capturing both long-range dislocation plasticity and short-range atomistic phenomena. The use of CADD permits for a clear study of the physical and mechanical influence of both complex plastic flow and non-continuum atomistic-level processes on the macroscopic response of material under indentation loading

Near-ideal strength in metal nanotubes revealed by atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Sun, Mingfei; Xiao, Fei [Department of Materials Science, Fudan University, 220 Handan Road, Shanghai 200433 (China); Deng, Chuang, E-mail: dengc@ad.umanitoba.ca [Department of Mechanical and Manufacturing Engineering, The University of Manitoba, 15Gillson Street, Winnipeg, Manitoba R3T 5V6 (Canada)

2013-12-02

Here we report extraordinary mechanical properties revealed by atomistic simulations in metal nanotubes with hollow interior that have been long overlooked. Particularly, the yield strength in [1 1 1] Au nanotubes is found to be up to 60% higher than the corresponding solid Au nanowire, which approaches the theoretical ideal strength in Au. Furthermore, a remarkable transition from sharp to smooth yielding is observed in Au nanotubes with decreasing wall thickness. The ultrahigh tensile strength in [1 1 1] Au nanotube might originate from the repulsive image force exerted by the interior surface against dislocation nucleation from the outer surface.

Spatio-temporal scaling effects on longshore sediment transport pattern along the nearshore zone

Science.gov (United States)

Khorram, Saeed; Ergil, Mustafa

2018-03-01

A measure of uncertainties, entropy has been employed in such different applications as coastal engineering probability inferences. Entropy sediment transport integration theories present novel visions in coastal analyses/modeling the application and development of which are still far-reaching. Effort has been made in the present paper to propose a method that needs an entropy-power index for spatio-temporal patterns analyses. Results have shown that the index is suitable for marine/hydrological ecosystem components analyses based on a beach area case study. The method makes use of six Makran Coastal monthly data (1970-2015) and studies variables such as spatio-temporal patterns, LSTR (long-shore sediment transport rate), wind speed, and wave height all of which are time-dependent and play considerable roles in terrestrial coastal investigations; the mentioned variables show meaningful spatio-temporal variability most of the time, but explanation of their combined performance is not easy. Accordingly, the use of an entropy-power index can show considerable signals that facilitate the evaluation of water resources and will provide an insight regarding hydrological parameters' interactions at scales as large as beach areas. Results have revealed that an STDDPI (entropy based spatio-temporal disorder dynamics power index) can simulate wave, long-shore sediment transport rate, and wind when granulometry, concentration, and flow conditions vary.

Self-evolving atomistic kinetic Monte Carlo: fundamentals and applications

International Nuclear Information System (INIS)

Xu Haixuan; Osetsky, Yuri N; Stoller, Roger E

2012-01-01

The fundamentals of the framework and the details of each component of the self-evolving atomistic kinetic Monte Carlo (SEAKMC) are presented. The strength of this new technique is the ability to simulate dynamic processes with atomistic fidelity that is comparable to molecular dynamics (MD) but on a much longer time scale. The observation that the dimer method preferentially finds the saddle point (SP) with the lowest energy is investigated and found to be true only for defects with high symmetry. In order to estimate the fidelity of dynamics and accuracy of the simulation time, a general criterion is proposed and applied to two representative problems. Applications of SEAKMC for investigating the diffusion of interstitials and vacancies in bcc iron are presented and compared directly with MD simulations, demonstrating that SEAKMC provides results that formerly could be obtained only through MD. The correlation factor for interstitial diffusion in the dumbbell configuration, which is extremely difficult to obtain using MD, is predicted using SEAKMC. The limitations of SEAKMC are also discussed. The paper presents a comprehensive picture of the SEAKMC method in both its unique predictive capabilities and technically important details.

Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations.

Science.gov (United States)

Paul, Fabian; Noé, Frank; Weikl, Thomas R

2018-03-27

Unstructured proteins and peptides typically fold during binding to ligand proteins. A challenging problem is to identify the mechanism and kinetics of these binding-induced folding processes in experiments and atomistic simulations. In this Article, we present a detailed picture for the folding of the inhibitor peptide PMI into a helix during binding to the oncoprotein fragment 25-109 Mdm2 obtained from atomistic, explicit-water simulations and Markov state modeling. We find that binding-induced folding of PMI is highly parallel and can occur along a multitude of pathways. Some pathways are induced-fit-like with binding occurring prior to PMI helix formation, while other pathways are conformational-selection-like with binding after helix formation. On the majority of pathways, however, binding is intricately coupled to folding, without clear temporal ordering. A central feature of these pathways is PMI motion on the Mdm2 surface, along the binding groove of Mdm2 or over the rim of this groove. The native binding groove of Mdm2 thus appears as an asymmetric funnel for PMI binding. Overall, binding-induced folding of PMI does not fit into the classical picture of induced fit or conformational selection that implies a clear temporal ordering of binding and folding events. We argue that this holds in general for binding-induced folding processes because binding and folding events in these processes likely occur on similar time scales and do exhibit the time-scale separation required for temporal ordering.

Atomistic simulation of the premelting of iron and aluminum : Implications for high-pressure melting-curve measurements

NARCIS (Netherlands)

Starikov, Sergey V.; Stegailov, Vladimir V.

2009-01-01

Using atomistic simulations we show the importance of the surface premelting phenomenon for the melting-curve measurements at high pressures. The model under consideration mimics the experimental conditions deployed for melting studies with diamond-anvil cells. The iron is considered in this work

Finite element analysis of an atomistically derived cohesive model for brittle fracture

International Nuclear Information System (INIS)

Lloyd, J T; McDowell, D L; Zimmerman, J A; Jones, R E; Zhou, X W

2011-01-01

In order to apply information from molecular dynamics (MD) simulations in problems governed by engineering length and time scales, a coarse graining methodology must be used. In previous work by Zhou et al (2009 Acta Mater. 57 4671–86), a traction-separation cohesive model was developed using results from MD simulations with atomistic-to-continuum measures of stress and displacement. Here, we implement this cohesive model within a combined finite element/cohesive surface element framework (referred to as a finite element approach or FEA), and examine the ability for the atomistically informed FEA to directly reproduce results from MD. We find that FEA shows close agreement of both stress and crack opening displacement profiles at the cohesive interface, although some differences do exist that can be attributed to the stochastic nature of finite temperature MD. The FEA methodology is then used to study slower loading rates that are computationally expensive for MD. We find that the crack growth process initially exhibits a rate-independent relationship between crack length and boundary displacement, followed by a rate-dependent regime where, at a given amount of boundary displacement, a lower applied strain rate produces a longer crack length. Our method is also extended to larger length scales by simulating a compact tension fracture-mechanics specimen with sub-micrometer dimensions. Such a simulation shows a computational speedup of approximately four orders of magnitude over conventional atomistic simulation, while exhibiting the expected fracture-mechanics response. Finally, differences between FEA and MD are explored with respect to ensemble and temperature effects in MD, and their impact on the cohesive model and crack growth behavior. These results enable us to make several recommendations to improve the methodology used to derive cohesive laws from MD simulations. In light of this work, which has critical implications for efforts to derive continuum laws

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

Science.gov (United States)

Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

Computer code for the atomistic simulation of lattice defects and dynamics

International Nuclear Information System (INIS)

Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

1980-04-01

This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability

Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

International Nuclear Information System (INIS)

Seppä, Jeremias; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Lassila, Antti; Reischl, Bernhard; Raiteri, Paolo; Rohl, Andrew L; Nordlund, Kai

2017-01-01

Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation. (paper)

Large-scale atomistic simulations of nanostructured materials based on divide-and-conquer density functional theory

Directory of Open Access Journals (Sweden)

Vashishta P.

2011-05-01

Full Text Available A linear-scaling algorithm based on a divide-and-conquer (DC scheme is designed to perform large-scale molecular-dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT. This scheme is applied to the thermite reaction at an Al/Fe2O3 interface. It is found that mass diffusion and reaction rate at the interface are enhanced by a concerted metal-oxygen flip mechanism. Preliminary simulations are carried out for an aluminum particle in water based on the conventional DFT, as a target system for large-scale DC-DFT simulations. A pair of Lewis acid and base sites on the aluminum surface preferentially catalyzes hydrogen production in a low activation-barrier mechanism found in the simulations

Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

Science.gov (United States)

Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kibaek

2017-01-01

We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link.

Degenerate Ising model for atomistic simulation of crystal-melt interfaces

Energy Technology Data Exchange (ETDEWEB)

Schebarchov, D., E-mail: Dmitri.Schebarchov@gmail.com [University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Schulze, T. P., E-mail: schulze@math.utk.edu [Department of Mathematics, University of Tennessee, Knoxville, Tennessee 37996-1300 (United States); Hendy, S. C. [The MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6140 (New Zealand); Department of Physics, University of Auckland, Auckland 1010 (New Zealand)

2014-02-21

One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quantifies the difference in communal entropy between the two phases. We simulate the (stochastic) evolution of this minimal model by applying rejection-free canonical and microcanonical Monte Carlo algorithms, and we obtain caloric curves and heat capacity plots for square (2D) and face-centred cubic (3D) lattices with periodic boundary conditions. Since the model admits precise adjustment of bulk latent heat and communal entropy, neither of which affect the interface properties, we are able to tune the crystal nucleation barriers at a fixed degree of undercooling and verify a dimension-dependent scaling expected from classical nucleation theory. We also analyse the equilibrium crystal-melt coexistence in the microcanonical ensemble, where we detect negative heat capacities and find that this phenomenon is more pronounced when the interface is the dominant contributor to the total entropy. The negative branch of the heat capacity appears smooth only when the equilibrium interface-area-to-volume ratio is not constant but varies smoothly with the excitation energy. Finally, we simulate microcanonical crystal nucleation and subsequent relaxation to an equilibrium Wulff shape, demonstrating the model's utility in tracking crystal-melt interfaces at the atomistic level.

Degenerate Ising model for atomistic simulation of crystal-melt interfaces

International Nuclear Information System (INIS)

Schebarchov, D.; Schulze, T. P.; Hendy, S. C.

2014-01-01

One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quantifies the difference in communal entropy between the two phases. We simulate the (stochastic) evolution of this minimal model by applying rejection-free canonical and microcanonical Monte Carlo algorithms, and we obtain caloric curves and heat capacity plots for square (2D) and face-centred cubic (3D) lattices with periodic boundary conditions. Since the model admits precise adjustment of bulk latent heat and communal entropy, neither of which affect the interface properties, we are able to tune the crystal nucleation barriers at a fixed degree of undercooling and verify a dimension-dependent scaling expected from classical nucleation theory. We also analyse the equilibrium crystal-melt coexistence in the microcanonical ensemble, where we detect negative heat capacities and find that this phenomenon is more pronounced when the interface is the dominant contributor to the total entropy. The negative branch of the heat capacity appears smooth only when the equilibrium interface-area-to-volume ratio is not constant but varies smoothly with the excitation energy. Finally, we simulate microcanonical crystal nucleation and subsequent relaxation to an equilibrium Wulff shape, demonstrating the model's utility in tracking crystal-melt interfaces at the atomistic level

Atomistic simulation of the coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface

Science.gov (United States)

Xiao, HuiFang; Huang, Bin; Yao, Ge; Kang, WenBin; Gong, Sheng; Pan, Hai; Cao, Yi; Wang, Jun; Zhang, Jian; Wang, Wei

2018-03-01

Understanding the processes of protein adsorption/desorption on nanoparticles' surfaces is important for the development of new nanotechnology involving biomaterials; however, an atomistic resolution picture for these processes and for the simultaneous protein conformational change is missing. Here, we report the adsorption of protein GB1 on a polystyrene nanoparticle surface using atomistic molecular dynamic simulations. Enabled by metadynamics, we explored the relevant phase space and identified three protein states, each involving both the adsorbed and desorbed modes. We also studied the change of the secondary and tertiary structures of GB1 during adsorption and the dominant interactions between the protein and surface in different adsorption stages. The results we obtained from simulation were found to be more adequate and complete than the previous one. We believe the model presented in this paper, in comparison with the previous ones, is a better theoretical model to understand and explain the experimental results.

Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc(1) complex

DEFF Research Database (Denmark)

Poyry, S.; Cramariuc, O.; Postila, P. A.

2013-01-01

by both ensuring the structural integrity of the protein complex and also by taking part in the proton uptake. Yet, the atom-scale understanding of these highly charged four-tail lipids in the cyt bc(1) function has remained quite unclear. We consider this issue through atomistic molecular dynamics...... the description of the role of the surrounding lipid environment: in addition to the specific CL-protein interactions, we observe the protein domains on the positive side of the membrane to settle against the lipids. Altogether, the simulations discussed in this article provide novel views into the dynamics...... simulations that are applied to the entire cyt bc(1) dimer of the purple photosynthetic bacterium Rhodobacter capsulatus embedded in a lipid bilayer. We find CLs to spontaneously diffuse to the dimer interface to the immediate vicinity of the higher potential heme b groups of the complex's catalytic Q...

Multiscale Simulations Using Particles

DEFF Research Database (Denmark)

Walther, Jens Honore

vortex methods for problems in continuum fluid dynamics, dissipative particle dynamics for flow at the meso scale, and atomistic molecular dynamics simulations of nanofluidic systems. We employ multiscale techniques to breach the atomistic and continuum scales to study fundamental problems in fluid...... dynamics. Recent work on the thermophoretic motion of water nanodroplets confined inside carbon nanotubes, and multiscale techniques for polar liquids will be discussed in detail at the symposium....

Thermodynamics of grain boundary premelting in alloys. II. Atomistic simulation

International Nuclear Information System (INIS)

Williams, P.L.; Mishin, Y.

2009-01-01

We apply the semi-grand-canonical Monte Carlo method with an embedded-atom potential to study grain boundary (GB) premelting in Cu-rich Cu-Ag alloys. The Σ5 GB chosen for this study becomes increasingly disordered near the solidus line while its local chemical composition approaches the liquidus composition at the same temperature. This behavior indicates the formation of a thin layer of the liquid phase in the GB when the grain composition approaches the solidus. The thickness of the liquid layer remains finite and the GB can be overheated/oversaturated to metastable states slightly above the solidus. The premelting behavior found by the simulations is qualitatively consistent with the phase-field model of the same binary system presented in Part I of this work [Mishin Y, Boettinger WJ, Warren JA, McFadden GB. Acta Mater, in press]. Although this agreement is encouraging, we discuss several problems arising when atomistic simulations are compared with phase-field modeling.

Relaxation of a steep density gradient in a simple fluid: Comparison between atomistic and continuum modeling

International Nuclear Information System (INIS)

Pourali, Meisam; Maghari, Ali; Meloni, Simone; Magaletti, Francesco; Casciola, Carlo Massimo; Ciccotti, Giovanni

2014-01-01

We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (∼10 times the molecular size). In presence of molecular scale features some of the continuum fields (e.g., density and momentum) are in good agreement with atomistic counterparts, but are smoother. On the contrary, other fields, such as the temperature field, present very large difference with respect to reference (atomistic) ones. This is due to the limited accuracy of some of the empirical relations used in continuum models, the equation of state of the fluid in the present example

Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

International Nuclear Information System (INIS)

Stukowski, Alexander

2010-01-01

The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations functions are integrated into its easy-to-use graphical user interface. The software is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface. It is distributed as open-source software and can be downloaded from the website http://ovito.sourceforge.net/

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

Science.gov (United States)

Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash;

Spatio-temporal Eigenvector Filtering: Application on Bioenergy Crop Impacts

Science.gov (United States)

Wang, M.; Kamarianakis, Y.; Georgescu, M.

2017-12-01

A suite of 10-year ensemble-based simulations was conducted to investigate the hydroclimatic impacts due to large-scale deployment of perennial bioenergy crops across the continental United States. Given the large size of the simulated dataset (about 60Tb), traditional hierarchical spatio-temporal statistical modelling cannot be implemented for the evaluation of physics parameterizations and biofuel impacts. In this work, we propose a filtering algorithm that takes into account the spatio-temporal autocorrelation structure of the data while avoiding spatial confounding. This method is used to quantify the robustness of simulated hydroclimatic impacts associated with bioenergy crops to alternative physics parameterizations and observational datasets. Results are evaluated against those obtained from three alternative Bayesian spatio-temporal specifications.

Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides

International Nuclear Information System (INIS)

Ogawa, Hiroshi

2015-01-01

Highlights: • Hydrogen–dislocation interaction was simulated by molecular dynamics method. • Different distribution of H atoms were observed at edge and screw dislocation. • Planner distribution of hydrogen may be caused by partialized edge dislocation. • Hydrogen diffusivity was reduced in both edge and screw dislocation models. • Pipe diffusion was observed for edge dislocation but not for screw dislocation. - Abstract: Kinetics of interstitial hydrogen atoms near dislocation cores were analyzed by atomistic simulation. Classical molecular dynamics method was applied to model structures of edge and screw dislocations in α-phase vanadium hydride. Simulation showed that hydrogen atoms aggregate near dislocation cores. The spatial distribution of hydrogen has a planner shape at edge dislocation due to dislocation partialization, and a cylindrical shape at screw dislocation. Simulated self-diffusion coefficients of hydrogen atoms in dislocation models were a half- to one-order lower than that of dislocation-free model. Arrhenius plot of self-diffusivity showed slightly different activation energies for edge and screw dislocations. Directional dependency of hydrogen diffusion near dislocation showed high and low diffusivity along edge and screw dislocation lines, respectively, hence so called ‘pipe diffusion’ possibly occur at edge dislocation but does not at screw dislocation

Lattice Thermal Conductivity of Ultra High Temperature Ceramics ZrB2 and HfB2 from Atomistic Simulations

Science.gov (United States)

Lawson, John W.; Murray, Daw S.; Bauschlicher, Charles W., Jr.

2011-01-01

Atomistic Green-Kubo simulations are performed to evaluate the lattice thermal conductivity for single crystals of the ultra high temperature ceramics ZrB2 and HfB2 for a range of temperatures. Recently developed interatomic potentials are used for these simulations. Heat current correlation functions show rapid oscillations which can be identified with mixed metal-Boron optical phonon modes. Agreement with available experimental data is good.

Atomistic spin dynamics simulations on Mn-doped GaAs and CuMn

Energy Technology Data Exchange (ETDEWEB)

Hellsvik, Johan, E-mail: johan.hellsvik@fysik.uu.s [Department of Physics and Materials Science, Uppsala University, Box 530, SE-751 21 Uppsala (Sweden)

2010-01-01

The magnetic dynamical behavior of two random alloys have been investigated in atomistic spin dynamics (ASD) simulations. For both materials, magnetic exchange parameters calculated with first principles electronic structure methods were used. From experiments it is well known that CuMn is a highly frustrated magnetic system and a good manifestation of a Heisenberg spin glass. In our ASD simulations the behavior of the autocorrelation function indicate spin glass behavior. The diluted magnetic semiconductor (DMS) Mn-doped GaAs is engineered with hopes of high enough Curie temperatures to operate in spintronic devices. Impurities such as As antisites and Mn interstitials change the exhange couplings from being mainly ferromagnetic to also have antiferromagnetic components. We explore how the resulting frustration affects the magnetization dynamics for a varying rate of As antisites.

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

KAUST Repository

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-01-01

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. © 2013 The Royal Society of Chemistry.

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

Science.gov (United States)

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

2016-12-01

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.

Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code

Energy Technology Data Exchange (ETDEWEB)

Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

1980-04-01

This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability.

A kinetic Monte Carlo simulation method of van der Waals epitaxy for atomistic nucleation-growth processes of transition metal dichalcogenides.

Science.gov (United States)

Nie, Yifan; Liang, Chaoping; Cha, Pil-Ryung; Colombo, Luigi; Wallace, Robert M; Cho, Kyeongjae

2017-06-07

Controlled growth of crystalline solids is critical for device applications, and atomistic modeling methods have been developed for bulk crystalline solids. Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW) heterostructures has not yet been developed. Specifically, the growth of single-layered transition metal dichalcogenides (TMDs) is currently facing tremendous challenges, and a detailed understanding based on KMC simulations would provide critical guidance to enable controlled growth of vdW heterostructures. In this work, a KMC simulation method is developed for the growth modeling on the vdW epitaxy of TMDs. The KMC method has introduced full material parameters for TMDs in bottom-up synthesis: metal and chalcogen adsorption/desorption/diffusion on substrate and grown TMD surface, TMD stacking sequence, chalcogen/metal ratio, flake edge diffusion and vacancy diffusion. The KMC processes result in multiple kinetic behaviors associated with various growth behaviors observed in experiments. Different phenomena observed during vdW epitaxy process are analysed in terms of complex competitions among multiple kinetic processes. The KMC method is used in the investigation and prediction of growth mechanisms, which provide qualitative suggestions to guide experimental study.

Dislocations and elementary processes of plasticity in FCC metals: atomic scale simulations

International Nuclear Information System (INIS)

Rodney, D.

2000-01-01

We present atomic-scale simulations of two elementary processes of FCC crystal plasticity. The first study consists in the simulation by molecular dynamics, in a nickel crystal, of the interactions between an edge dislocation and glissile interstitial loops of the type that form under irradiation in displacement cascades. The simulations show various atomic-scale interaction processes leading to the absorption and drag of the loops by the dislocation. These reactions certainly contribute to the formation of the 'clear bands' observed in deformed irradiated materials. The simulations also allow to study quantitatively the role of the glissile loops in irradiation hardening. In particular, dislocation unpinning stresses for certain pinning mechanisms are evaluated from the simulations. The second study consists first in the generalization in three dimensions of the quasi-continuum method (QCM), a multi-scale simulation method which couples atomistic techniques and the finite element method. In the QCM, regions close to dislocation cores are simulated at the atomic-scale while the rest of the crystal is simulated with a lower resolution by means of a discretization of the displacement fields using the finite element method. The QCM is then tested on the simulation of the formation and breaking of dislocation junctions in an aluminum crystal. Comparison of the simulations with an elastic model of dislocation junctions shows that the structure and strength of the junctions are dominated by elastic line tension effects, as is assumed in classical theories. (author)

Insights into the charge carrier terahertz mobility in polyfluorenes from large-scale atomistic simulations and time-resolved terahertz spectroscopy

Czech Academy of Sciences Publication Activity Database

Vukmirović, N.; Ponseca, C.S.; Němec, Hynek; Yartsev, A.; Sundström, V.

2012-01-01

Roč. 116, č. 37 (2012), s. 19665-1972 ISSN 1932-7447 Institutional research plan: CEZ:AV0Z10100520 Keywords : charge carrier mobility * time-resolved terahertz spectroscopy * multiscale atomistic calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.814, year: 2012

Atomistic Simulation of Intrinsic Defects and Trivalent and Tetravalent Ion Doping in Hydroxyapatite

Directory of Open Access Journals (Sweden)

Ricardo D. S. Santos

2014-01-01

Full Text Available Atomistic simulation techniques have been employed in order to investigate key issues related to intrinsic defects and a variety of dopants from trivalent and tetravalent ions. The most favorable intrinsic defect is determined to be a scheme involving calcium and hydroxyl vacancies. It is found that trivalent ions have an energetic preference for the Ca site, while tetravalent ions can enter P sites. Charge compensation is predicted to occur basically via three schemes. In general, the charge compensation via the formation of calcium vacancies is more favorable. Trivalent dopant ions are more stable than tetravalent dopants.

Optimal kernel shape and bandwidth for atomistic support of continuum stress

International Nuclear Information System (INIS)

Ulz, Manfred H; Moran, Sean J

2013-01-01

The treatment of atomistic scale interactions via molecular dynamics simulations has recently found favour for multiscale modelling within engineering. The estimation of stress at a continuum point on the atomistic scale requires a pre-defined kernel function. This kernel function derives the stress at a continuum point by averaging the contribution from atoms within a region surrounding the continuum point. This averaging volume, and therefore the associated stress at a continuum point, is highly dependent on the bandwidth and shape of the kernel. In this paper we propose an effective and entirely data-driven strategy for simultaneously computing the optimal shape and bandwidth for the kernel. We thoroughly evaluate our proposed approach on copper using three classical elasticity problems. Our evaluation yields three key findings: firstly, our technique can provide a physically meaningful estimation of kernel bandwidth; secondly, we show that a uniform kernel is preferred, thereby justifying the default selection of this kernel shape in future work; and thirdly, we can reliably estimate both of these attributes in a data-driven manner, obtaining values that lead to an accurate estimation of the stress at a continuum point. (paper)

Atomistic simulations of screw dislocations in bcc tungsten: From core structures and static properties to interaction with vacancies

Energy Technology Data Exchange (ETDEWEB)

Xu, Ke [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Niu, Liang-Liang [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Department of Nuclear Engineering and Radiological Science, University of Michigan, Ann Arbor, MI 48109 (United States); Jin, Shuo, E-mail: jinshuo@buaa.edu.cn [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Shu, Xiaolin [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China); Xie, Hongxian [School of Mechanical Engineering, Hebei University of Technology, Tianjin 300132 (China); Wang, Lifang; Lu, Guang-Hong [School of Physics and Nuclear Energy Engineering, Beihang University, Beijing 100191 (China); Beijing Key Laboratory of Advanced Nuclear Materials and Physics, Beihang University, Beijing 100191 (China)

2017-02-15

Atomistic simulations have been used to investigate the core structures, static properties of isolated 1/2 <1 1 1> screw dislocations, and their interaction with vacancies in bcc tungsten (W) based on three empirical interatomic potentials. Differential displacement maps show that only one embedded atom method potential is able to reproduce the compact non-degenerate core as evidenced by ab initio calculations. The obtained strain energy and stress distribution from atomistic simulations are, in general, consistent with elasticity theory predictions. In particular, one component of the calculated shear stress, which is not present according to elasticity theory, is non-negligible in the core region of our dislocation model. The differences between the results calculated from three interatomic potentials are in details, such as the specific value and the symmetry, but the trend of spatial distributions of static properties in the long range are close to each other. By calculating the binding energies between the dislocations and vacancies, we demonstrate that the dislocations act as vacancy sinks, which may be important for the nucleation and growth of hydrogen bubbles in W under irradiation.

Atomistic minimal model for estimating profile of electrodeposited nanopatterns

Science.gov (United States)

Asgharpour Hassankiadeh, Somayeh; Sadeghi, Ali

2018-06-01

We develop a computationally efficient and methodologically simple approach to realize molecular dynamics simulations of electrodeposition. Our minimal model takes into account the nontrivial electric field due a sharp electrode tip to perform simulations of the controllable coating of a thin layer on a surface with an atomic precision. On the atomic scale a highly site-selective electrodeposition of ions and charged particles by means of the sharp tip of a scanning probe microscope is possible. A better understanding of the microscopic process, obtained mainly from atomistic simulations, helps us to enhance the quality of this nanopatterning technique and to make it applicable in fabrication of nanowires and nanocontacts. In the limit of screened inter-particle interactions, it is feasible to run very fast simulations of the electrodeposition process within the framework of the proposed model and thus to investigate how the shape of the overlayer depends on the tip-sample geometry and dielectric properties, electrolyte viscosity, etc. Our calculation results reveal that the sharpness of the profile of a nano-scale deposited overlayer is dictated by the normal-to-sample surface component of the electric field underneath the tip.

Simulating smoke transport from wildland fires with a regional-scale air quality model: sensitivity to spatiotemporal allocation of fire emissions.

Science.gov (United States)

Garcia-Menendez, Fernando; Hu, Yongtao; Odman, Mehmet T

2014-09-15

Air quality forecasts generated with chemical transport models can provide valuable information about the potential impacts of fires on pollutant levels. However, significant uncertainties are associated with fire-related emission estimates as well as their distribution on gridded modeling domains. In this study, we explore the sensitivity of fine particulate matter concentrations predicted by a regional-scale air quality model to the spatial and temporal allocation of fire emissions. The assessment was completed by simulating a fire-related smoke episode in which air quality throughout the Atlanta metropolitan area was affected on February 28, 2007. Sensitivity analyses were carried out to evaluate the significance of emission distribution among the model's vertical layers, along the horizontal plane, and into hourly inputs. Predicted PM2.5 concentrations were highly sensitive to emission injection altitude relative to planetary boundary layer height. Simulations were also responsive to the horizontal allocation of fire emissions and their distribution into single or multiple grid cells. Additionally, modeled concentrations were greatly sensitive to the temporal distribution of fire-related emissions. The analyses demonstrate that, in addition to adequate estimates of emitted mass, successfully modeling the impacts of fires on air quality depends on an accurate spatiotemporal allocation of emissions. Copyright © 2014 Elsevier B.V. All rights reserved.

A method of integration of atomistic simulations and continuum mechanics by collecting of dynamical systems with dimensional reduction

International Nuclear Information System (INIS)

Kaczmarek, J.

2002-01-01

Elementary processes responsible for phenomena in material are frequently related to scale close to atomic one. Therefore atomistic simulations are important for material sciences. On the other hand continuum mechanics is widely applied in mechanics of materials. It seems inevitable that both methods will gradually integrate. A multiscale method of integration of these approaches called collection of dynamical systems with dimensional reduction is introduced in this work. The dimensional reduction procedure realizes transition between various scale models from an elementary dynamical system (EDS) to a reduced dynamical system (RDS). Mappings which transform variables and forces, skeletal dynamical system (SDS) and a set of approximation and identification methods are main components of this procedure. The skeletal dynamical system is a set of dynamical systems parameterized by some constants and has variables related to the dimensionally reduced model. These constants are identified with the aid of solutions of the elementary dynamical system. As a result we obtain a dimensionally reduced dynamical system which describes phenomena in an averaged way in comparison with the EDS. Concept of integration of atomistic simulations with continuum mechanics consists in using a dynamical system describing evolution of atoms as an elementary dynamical system. Then, we introduce a continuum skeletal dynamical system within the dimensional reduction procedure. In order to construct such a system we have to modify a continuum mechanics formulation to some degree. Namely, we formalize scale of averaging for continuum theory and as a result we consider continuum with finite-dimensional fields only. Then, realization of dimensional reduction is possible. A numerical example of realization of the dimensional reduction procedure is shown. We consider a one dimensional chain of atoms interacting by Lennard-Jones potential. Evolution of this system is described by an elementary

Single asperity nanocontacts: Comparison between molecular dynamics simulations and continuum mechanics models

NARCIS (Netherlands)

Solhjoo, Soheil; Vakis, Antonis I.

Abstract Using classical molecular dynamics, atomic scale simulations of normal contact between a nominally flat substrate and different atomistic and non-atomistic spherical particles were performed to investigate the applicability of classical contact theories at the nanoscale, and further

Molecular modeling and simulation of atactic polystyrene/amorphous silica nanocomposites

International Nuclear Information System (INIS)

Mathioudakis, I; Vogiatzis, G G; Tzoumanekas, C; Theodorou, D N

2016-01-01

The local structure, segmental dynamics, topological analysis of entanglement networks and mechanical properties of atactic polystyrene - amorphous silica nanocomposites are studied via molecular simulations using two interconnected levels of representation: (a) A coarse - grained level. Equilibration at all length scales at this level is achieved via connectivity - altering Monte Carlo simulations. (b) An atomistic level. Initial configurations for atomistic Molecular Dynamics (MD) simulations are obtained by reverse mapping well- equilibrated coarse-grained configurations. By analyzing atomistic MD trajectories, the polymer density profile is found to exhibit layering in the vicinity of the nanoparticle surface. The dynamics of polystyrene (in neat and filled melt systems) is characterized in terms of bond orientation. Well-equilibrated coarse-grained long-chain configurations are reduced to entanglement networks via topological analysis with the CReTA algorithm. Atomistic simulation results for the mechanical properties are compared to the experimental measurements and other computational works. (paper)

Constraint methods that accelerate free-energy simulations of biomolecules.

Science.gov (United States)

Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A

2015-12-28

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

Full-Scale Approximations of Spatio-Temporal Covariance Models for Large Datasets

KAUST Repository

Zhang, Bohai; Sang, Huiyan; Huang, Jianhua Z.

2014-01-01

of dataset and application of such models is not feasible for large datasets. This article extends the full-scale approximation (FSA) approach by Sang and Huang (2012) to the spatio-temporal context to reduce computational complexity. A reversible jump Markov

Transfer of spatio-temporal multifractal properties of rainfall to simulated surface runoff

Science.gov (United States)

Gires, Auguste; Giangola-Murzyn, Agathe; Richard, Julien; Abbes, Jean-Baptiste; Tchiguirinskaia, Ioulia; Schertzer, Daniel; Willinger, Bernard; Cardinal, Hervé; Thouvenot, Thomas

2014-05-01

In this paper we suggest to use scaling laws and more specifically Universal Multifractals (UM) to analyse in a spatio-temporal framework both the radar rainfall and the simulated surface runoff. Such tools have been extensively used to analyse and simulate geophysical fields extremely variable over wide range of spatio-temporal scales such as rainfall, but have not often if ever been applied to surface runoff. Such novel combined analysis helps to improve the understanding of the rainfall-runoff relationship. Two catchments of the chair "Hydrology for resilient cities" sponsored by Véolia, and of the European Interreg IV RainGain project are used. They are both located in the Paris area: a 144 ha flat urban area in the Seine-Saint-Denis County, and a 250 ha urban area with a significant portion of forest located on a steep hillside of the Bièvre River. A fully distributed urban hydrological model currently under development called Multi-Hydro is implemented to represent the catchments response. It consists in an interacting core between open source software packages, each of them representing a portion of the water cycle in urban environment. The fully distributed model is tested with pixels of size 5, 10 and 20 m. In a first step the model is validated for three rainfall events that occurred in 2010 and 2011, for which the Météo-France radar mosaic with a resolution of 1 km in space and 5 min in time is available. These events generated significant surface runoff and some local flooding. The sensitivity of the model to the rainfall resolution is briefly checked by stochastically generating an ensemble of realistic downscaled rainfall fields (obtained by continuing the underlying cascade process which is observed on the available range of scales) and inputting them into the model. The impact is significant on both the simulated sewer flow and surface runoff. Then rainfall fields are generated with the help of discrete multifractal cascades and inputted in the

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

Science.gov (United States)

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

Large-scale computing with Quantum Espresso

International Nuclear Information System (INIS)

Giannozzi, P.; Cavazzoni, C.

2009-01-01

This paper gives a short introduction to Quantum Espresso: a distribution of software for atomistic simulations in condensed-matter physics, chemical physics, materials science, and to its usage in large-scale parallel computing.

Addressing uncertainty in atomistic machine learning

DEFF Research Database (Denmark)

Peterson, Andrew A.; Christensen, Rune; Khorshidi, Alireza

2017-01-01

Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility of the predi......Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility...... of the predictions. In this perspective, we address the types of errors that might arise in atomistic machine learning, the unique aspects of atomistic simulations that make machine-learning challenging, and highlight how uncertainty analysis can be used to assess the validity of machine-learning predictions. We...... suggest this will allow researchers to more fully use machine learning for the routine acceleration of large, high-accuracy, or extended-time simulations. In our demonstrations, we use a bootstrap ensemble of neural network-based calculators, and show that the width of the ensemble can provide an estimate...

Spatiotemporal characteristics of heat waves over China in regional climate simulations within the CORDEX-EA project

Science.gov (United States)

Wang, Pinya; Tang, Jianping; Sun, Xuguang; Liu, Jianyong; Juan, Fang

2018-03-01

Using the Weather Research and Forecasting (WRF) model, this paper analyzes the spatiotemporal features of heat waves in 20-year regional climate simulations over East Asia, and investigates the capability of WRF to reproduce observational heat waves in China. Within the framework of the Coordinated Regional Climate Downscaling Experiment (CORDEX), the WRF model is driven by the ERA-Interim (ERAIN) reanalysis, and five continuous simulations are conducted from 1989 to 2008. Of these, four runs apply the interior spectral nudging (SN) technique with different wavenumbers, nudging variables and nudging coefficients. Model validations show that WRF can reasonably reproduce the spatiotemporal features of heat waves in China. Compared with the experiment without SN, the application of SN is effectie on improving the skill of the model in simulating both the spatial distributions and temporal variations of heat waves of different intensities. The WRF model shows advantages in reproducing the synoptic circulations with SN and therefore yields better representations for heat wave events. Besides, the SN method is able to preserve the variability of large-scale circulations quite well, which in turn adjusts the extreme temperature variability towards the observation. Among the four SN experiments, those with stronger nudging coefficients perform better in modulating both the spatial and temporal features of heat waves. In contrast, smaller nudging coefficients weaken the effects of SN on improving WRF's performances.

Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales.

Science.gov (United States)

Mukherjee, Biswaroop; Peter, Christine; Kremer, Kurt

2017-09-21

Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.

Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales

Science.gov (United States)

Mukherjee, Biswaroop; Peter, Christine; Kremer, Kurt

2017-09-01

Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.

Large-Scale Reactive Atomistic Simulation of Shock-induced Initiation Processes in Energetic Materials

Science.gov (United States)

Thompson, Aidan

2013-06-01

Initiation in energetic materials is fundamentally dependent on the interaction between a host of complex chemical and mechanical processes, occurring on scales ranging from intramolecular vibrations through molecular crystal plasticity up to hydrodynamic phenomena at the mesoscale. A variety of methods (e.g. quantum electronic structure methods (QM), non-reactive classical molecular dynamics (MD), mesoscopic continuum mechanics) exist to study processes occurring on each of these scales in isolation, but cannot describe how these processes interact with each other. In contrast, the ReaxFF reactive force field, implemented in the LAMMPS parallel MD code, allows us to routinely perform multimillion-atom reactive MD simulations of shock-induced initiation in a variety of energetic materials. This is done either by explicitly driving a shock-wave through the structure (NEMD) or by imposing thermodynamic constraints on the collective dynamics of the simulation cell e.g. using the Multiscale Shock Technique (MSST). These MD simulations allow us to directly observe how energy is transferred from the shockwave into other processes, including intramolecular vibrational modes, plastic deformation of the crystal, and hydrodynamic jetting at interfaces. These processes in turn cause thermal excitation of chemical bonds leading to initial chemical reactions, and ultimately to exothermic formation of product species. Results will be presented on the application of this approach to several important energetic materials, including pentaerythritol tetranitrate (PETN) and ammonium nitrate/fuel oil (ANFO). In both cases, we validate the ReaxFF parameterizations against QM and experimental data. For PETN, we observe initiation occurring via different chemical pathways, depending on the shock direction. For PETN containing spherical voids, we observe enhanced sensitivity due to jetting, void collapse, and hotspot formation, with sensitivity increasing with void size. For ANFO, we

Mechanisms of recognition and binding of α-TTP to the plasma membrane by multi-scale molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Christos eLamprakis

2015-07-01

Full Text Available We used multiple sets of simulations both at the atomistic and coarse-grained level of resolution, to investigate interaction and binding of α-tochoperol transfer protein (α-TTP to phosphatidylinositol phosphate lipids (PIPs. Our calculations indicate that enrichment of membranes with such lipids facilitate membrane anchoring. Atomistic models suggest that PIP can be incorporated into the binding cavity of α-TTP and therefore confirm that such protein can work as lipid exchanger between the endosome and the plasma membrane. Comparison of the atomistic models of the α-TTP / PIPs complex with membrane-bound α-TTP revealed different roles for the various basic residues composing the basic patch that is key for the protein / ligand interaction. Such residues are of critical importance as several point mutations at their position lead to severe forms of ataxia with vitamin E deficiency (AVED phenotypes. Specifically, R221 is main residue responsible for the stabilisation of the complex. R68 and R192 exchange strong interactions in the protein or in the membrane complex only, suggesting that the two residues alternate contact formation, thus facilitating lipid flipping from the membrane into the protein cavity during the lipid exchange process. Finally, R59 shows weaker interactions with PIPs anyway with a clear preference for specific phosphorylation positions, hinting a role in early membrane selectivity for the protein. Altogether, our simulations reveal significant aspects at the atomistic scale of interactions of α-TTP with the plasma membrane and with PIP, providing clarifications on the mechanism of intracellular vitamin E trafficking and helping establishing the role of key residue for the functionality of α-TTP.

Spatiotemporal property and predictability of large-scale human mobility

Science.gov (United States)

Zhang, Hai-Tao; Zhu, Tao; Fu, Dongfei; Xu, Bowen; Han, Xiao-Pu; Chen, Duxin

2018-04-01

Spatiotemporal characteristics of human mobility emerging from complexity on individual scale have been extensively studied due to the application potential on human behavior prediction and recommendation, and control of epidemic spreading. We collect and investigate a comprehensive data set of human activities on large geographical scales, including both websites browse and mobile towers visit. Numerical results show that the degree of activity decays as a power law, indicating that human behaviors are reminiscent of scale-free random walks known as Lévy flight. More significantly, this study suggests that human activities on large geographical scales have specific non-Markovian characteristics, such as a two-segment power-law distribution of dwelling time and a high possibility for prediction. Furthermore, a scale-free featured mobility model with two essential ingredients, i.e., preferential return and exploration, and a Gaussian distribution assumption on the exploration tendency parameter is proposed, which outperforms existing human mobility models under scenarios of large geographical scales.

Atomistic simulation of fatigue in face centred cubic metals

International Nuclear Information System (INIS)

Fan, Zhengxuan

2016-01-01

Fatigue is one of the major damage mechanisms of metals. It is characterized by strong environmental effects and wide lifetime dispersions which must be better understood. Different face centred cubic metals, al, Cu, Ni, and Ag are analyzed. The mechanical behaviour of surface steps naturally created by the glide of dislocations subjected to cyclic loading is examined using molecular dynamics simulations in vacuum and in air for Cu and Ni. an atomistic reconstruction phenomenon is observed at these surface steps which can induce strong irreversibility. Three different mechanisms of reconstruction are defined. Surface slip irreversibility under cyclic loading is analyzed. all surface steps are intrinsically irreversible under usual fatigue laboratory loading amplitude without the arrival of opposite sign dislocations on direct neighbor plane.With opposite sign dislocations on non direct neighbour planes, irreversibility cumulates cycle by cycle and a micro-notch is produced whose depth gradually increases.Oxygen environment affects the surface (first stage of oxidation) but does not lead to higher irreversibility as it has no major influence on the different mechanisms linked to surface relief evolution.a rough estimation of surface irreversibility is carried out for pure edge dislocations in persistent slip bands in so-called wavy materials. It gives an irreversibility fraction between 0.5 and 0.75 in copper in vacuum and in air, in agreement with recent atomic force microscopy measurements.Crack propagation mechanisms are simulated in inert environment. Cracks can propagate owing to the irreversibility of generated dislocations because of their mutual interactions up to the formation of dislocation junctions. (author) [fr

Fine Scale Spatiotemporal Clustering of Dengue Virus Transmission in Children and Aedes aegypti in Rural Thai Villages

NARCIS (Netherlands)

Yoon, I.K.; Getis, A.; Aldstadt, J.; Rothman, A.L.; Tannitisupawong, D.; Koenraadt, C.J.M.; Fansiri, T.; Jones, J.W.; Morrison, A.C.; Jarman, R.G.; Nisalak, A.; Mammen Jr., M.P.; Thammapalo, S.; Srikiatkhachorn, A.; Green, S.; Libraty, D.H.; Gibbons, R.V.; Endy, T.; Pimgate, C.; Scott, T.W.

2012-01-01

Background Based on spatiotemporal clustering of human dengue virus (DENV) infections, transmission is thought to occur at fine spatiotemporal scales by horizontal transfer of virus between humans and mosquito vectors. To define the dimensions of local transmission and quantify the factors that

Variational assimilation of streamflow into operational distributed hydrologic models: effect of spatiotemporal adjustment scale

Science.gov (United States)

Lee, H.; Seo, D.-J.; Liu, Y.; Koren, V.; McKee, P.; Corby, R.

2012-01-01

State updating of distributed rainfall-runoff models via streamflow assimilation is subject to overfitting because large dimensionality of the state space of the model may render the assimilation problem seriously under-determined. To examine the issue in the context of operational hydrology, we carry out a set of real-world experiments in which streamflow data is assimilated into gridded Sacramento Soil Moisture Accounting (SAC-SMA) and kinematic-wave routing models of the US National Weather Service (NWS) Research Distributed Hydrologic Model (RDHM) with the variational data assimilation technique. Study basins include four basins in Oklahoma and five basins in Texas. To assess the sensitivity of data assimilation performance to dimensionality reduction in the control vector, we used nine different spatiotemporal adjustment scales, where state variables are adjusted in a lumped, semi-distributed, or distributed fashion and biases in precipitation and potential evaporation (PE) are adjusted hourly, 6-hourly, or kept time-invariant. For each adjustment scale, three different streamflow assimilation scenarios are explored, where streamflow observations at basin interior points, at the basin outlet, or at both interior points and the outlet are assimilated. The streamflow assimilation experiments with nine different basins show that the optimum spatiotemporal adjustment scale varies from one basin to another and may be different for streamflow analysis and prediction in all of the three streamflow assimilation scenarios. The most preferred adjustment scale for seven out of nine basins is found to be the distributed, hourly scale, despite the fact that several independent validation results at this adjustment scale indicated the occurrence of overfitting. Basins with highly correlated interior and outlet flows tend to be less sensitive to the adjustment scale and could benefit more from streamflow assimilation. In comparison to outlet flow assimilation, interior flow

Harbour porpoise distribution can vary at small spatiotemporal scales in energetic habitats

Science.gov (United States)

Benjamins, Steven; van Geel, Nienke; Hastie, Gordon; Elliott, Jim; Wilson, Ben

2017-07-01

Marine habitat heterogeneity underpins species distribution and can be generated through interactions between physical and biological drivers at multiple spatiotemporal scales. Passive acoustic monitoring (PAM) is used worldwide to study potential impacts of marine industrial activities on cetaceans, but understanding of animals' site use at small spatiotemporal scales (marine renewable energy development (MRED) sites was investigated by deploying dense arrays of C-POD passive acoustic detectors at a wave energy test site (the European Marine Energy Centre [Billia Croo, Orkney]) and by a minor tidal-stream site (Scarba [Inner Hebrides]). Respective arrays consisted of 7 and 11 moorings containing two C-PODs each and were deployed for up to 55 days. Minimum inter-mooring distances varied between 300-600 m. All C-POD data were analysed at a temporal resolution of whole minutes, with each minute classified as 1 or 0 on the basis of presence/absence of porpoise click trains (Porpoise-Positive Minutes/PPMs). Porpoise detection rates were analysed using Generalised Additive Models (GAMs) with Generalised Estimation Equations (GEEs). Although there were many porpoise detections (wave test site: N=3,432; tidal-stream site: N=17,366), daily detection rates varied significantly within both arrays. Within the wave site array (<1 km diameter), average daily detection rates varied from 4.3 to 14.8 PPMs/day. Within the tidal-stream array (<2 km diameter), average daily detection rates varied from 10.3 to 49.7 PPMs/day. GAM-GEE model results for individual moorings within both arrays indicated linkages between porpoise presence and small-scale heterogeneity among different environmental covariates (e.g., tidal phase, time of day). Porpoise detection rates varied considerably but with coherent patterns between moorings only several hundred metres apart and within hours. These patterns presumably have ecological relevance. These results indicate that, in energetically active and

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

Science.gov (United States)

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

An atomistic methodology of energy release rate for graphene at nanoscale

International Nuclear Information System (INIS)

Zhang, Zhen; Lee, James D.; Wang, Xianqiao

2014-01-01

Graphene is a single layer of carbon atoms packed into a honeycomb architecture, serving as a fundamental building block for electric devices. Understanding the fracture mechanism of graphene under various conditions is crucial for tailoring the electrical and mechanical properties of graphene-based devices at atomic scale. Although most of the fracture mechanics concepts, such as stress intensity factors, are not applicable in molecular dynamics simulation, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at nanoscale. This work introduces an atomistic simulation methodology, based on the energy release rate, as a tool to unveil the fracture mechanism of graphene at nanoscale. This methodology can be easily extended to any atomistic material system. We have investigated both opening mode and mixed mode at different temperatures. Simulation results show that the critical energy release rate of graphene is independent of initial crack length at low temperature. Graphene with inclined pre-crack possesses higher fracture strength and fracture deformation but smaller critical energy release rate compared with the graphene with vertical pre-crack. Owing to its anisotropy, graphene with armchair chirality always has greater critical energy release rate than graphene with zigzag chirality. The increase of temperature leads to the reduction of fracture strength, fracture deformation, and the critical energy release rate of graphene. Also, higher temperature brings higher randomness of energy release rate of graphene under a variety of predefined crack lengths. The energy release rate is independent of the strain rate as long as the strain rate is small enough

Exploring Multi-Scale Spatiotemporal Twitter User Mobility Patterns with a Visual-Analytics Approach

Directory of Open Access Journals (Sweden)

Junjun Yin

2016-10-01

Full Text Available Understanding human mobility patterns is of great importance for urban planning, traffic management, and even marketing campaign. However, the capability of capturing detailed human movements with fine-grained spatial and temporal granularity is still limited. In this study, we extracted high-resolution mobility data from a collection of over 1.3 billion geo-located Twitter messages. Regarding the concerns of infringement on individual privacy, such as the mobile phone call records with restricted access, the dataset is collected from publicly accessible Twitter data streams. In this paper, we employed a visual-analytics approach to studying multi-scale spatiotemporal Twitter user mobility patterns in the contiguous United States during the year 2014. Our approach included a scalable visual-analytics framework to deliver efficiency and scalability in filtering large volume of geo-located tweets, modeling and extracting Twitter user movements, generating space-time user trajectories, and summarizing multi-scale spatiotemporal user mobility patterns. We performed a set of statistical analysis to understand Twitter user mobility patterns across multi-level spatial scales and temporal ranges. In particular, Twitter user mobility patterns measured by the displacements and radius of gyrations of individuals revealed multi-scale or multi-modal Twitter user mobility patterns. By further studying such mobility patterns in different temporal ranges, we identified both consistency and seasonal fluctuations regarding the distance decay effects in the corresponding mobility patterns. At the same time, our approach provides a geo-visualization unit with an interactive 3D virtual globe web mapping interface for exploratory geo-visual analytics of the multi-level spatiotemporal Twitter user movements.

Evolution of spatio-temporal drought characteristics: validation, projections and effect of adaptation scenarios

Science.gov (United States)

Vidal, J.-P.; Martin, E.; Kitova, N.; Najac, J.; Soubeyroux, J.-M.

2012-08-01

Drought events develop in both space and time and they are therefore best described through summary joint spatio-temporal characteristics, such as mean duration, mean affected area and total magnitude. This paper addresses the issue of future projections of such characteristics of drought events over France through three main research questions: (1) Are downscaled climate projections able to simulate spatio-temporal characteristics of meteorological and agricultural droughts in France over a present-day period? (2) How such characteristics will evolve over the 21st century? (3) How to use standardized drought indices to represent theoretical adaptation scenarios? These questions are addressed using the Isba land surface model, downscaled climate projections from the ARPEGE General Circulation Model under three emissions scenarios, as well as results from a previously performed 50-yr multilevel and multiscale drought reanalysis over France. Spatio-temporal characteristics of meteorological and agricultural drought events are computed using the Standardized Precipitation Index and the Standardized Soil Wetness Index, respectively, and for time scales of 3 and 12 months. Results first show that the distributions of joint spatio-temporal characteristics of observed events are well simulated by the downscaled hydroclimate projections over a present-day period. All spatio-temporal characteristics of drought events are then found to dramatically increase over the 21st century, with stronger changes for agricultural droughts. Two theoretical adaptation scenarios are eventually built based on hypotheses of adaptation to evolving climate and hydrological normals, either retrospective or prospective. The perceived spatio-temporal characteristics of drought events derived from these theoretical adaptation scenarios show much reduced changes, but they call for more realistic scenarios at both the catchment and national scale in order to accurately assess the combined effect of

Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Orlowski, A.; St-Pierre, J. F.; Magarkar, A.

2011-01-01

We used atomistic simulations to study the membrane-bound form of catechol-O-methyltransferase (MB-COMT). In particular we investigated the 26-residue transmembrane a-helical segment of MB-COMT together with the 24-residue fragment that links the transmembrane component to the main protein unit...... that was not included in our model. In numerous independent simulations we observed the formation of a salt bridge between ARC 27 and GLU40. The salt bridge closed the flexible loop that formed in the linker and kept it in the vicinity of the membrane-water interface. All simulations supported this conclusion...... that the linker has a clear affinity for the interface and preferentially arranges its residues to reside next to the membrane, without a tendency to relocate into the water phase. Furthermore, an extensive analysis of databases for sequences of membrane proteins that have a single transmembrane helical segment...

Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

Science.gov (United States)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

Multi-scale properties of large eddy simulations: correlations between resolved-scale velocity-field increments and subgrid-scale quantities

Science.gov (United States)

Linkmann, Moritz; Buzzicotti, Michele; Biferale, Luca

2018-06-01

We provide analytical and numerical results concerning multi-scale correlations between the resolved velocity field and the subgrid-scale (SGS) stress-tensor in large eddy simulations (LES). Following previous studies for Navier-Stokes equations, we derive the exact hierarchy of LES equations governing the spatio-temporal evolution of velocity structure functions of any order. The aim is to assess the influence of the subgrid model on the inertial range intermittency. We provide a series of predictions, within the multifractal theory, for the scaling of correlation involving the SGS stress and we compare them against numerical results from high-resolution Smagorinsky LES and from a-priori filtered data generated from direct numerical simulations (DNS). We find that LES data generally agree very well with filtered DNS results and with the multifractal prediction for all leading terms in the balance equations. Discrepancies are measured for some of the sub-leading terms involving cross-correlation between resolved velocity increments and the SGS tensor or the SGS energy transfer, suggesting that there must be room to improve the SGS modelisation to further extend the inertial range properties for any fixed LES resolution.

Theta variation and spatiotemporal scaling along the septotemporal axis of the hippocampus

Directory of Open Access Journals (Sweden)

Lauren L Long

2015-03-01

Full Text Available Hippocampal theta has been related to locomotor speed, attention, anxiety, sensorimotor integration and memory among other emergent phenomena. One difficulty in understanding the function of theta is that the hippocampus (HPC modulates voluntary behavior at the same time that it processes sensory input. Both functions are correlated with characteristic changes in theta indices. The current review highlights a series of studies examining theta local field potential (LFP signals across the septotemporal or longitudinal axis of the HPC. While the theta signal is coherent throughout the entirety of the HPC, the amplitude, but not the frequency, of theta varies significantly across its three-dimensional expanse. We suggest that the theta signal offers a rich vein of information about how distributed neuronal ensembles support emergent function. Further, we speculate that emergent function across the long axis varies with respect to spatiotemporal scale. Thus, septal hippocampus processes details of the proximal spatiotemporal environment while more temporal aspects process larger spaces and wider time-scales. The degree to which emergent functions are supported by the synchronization of theta across the septotemporal axis is an open question. Our working model is that theta synchrony serves to bind ensembles representing varying resolutions of spatiotemporal information at interdependent septotemporal areas of the HPC. Such synchrony and cooperative interactions along the septotemporal axis likely support memory formation and subsequent consolidation and retrieval.

Atomistic Modeling of Corrosion Events at the Interface between a Metal and Its Environment

Directory of Open Access Journals (Sweden)

Christopher D. Taylor

2012-01-01

Full Text Available Atomistic simulation is a powerful tool for probing the structure and properties of materials and the nature of chemical reactions. Corrosion is a complex process that involves chemical reactions occurring at the interface between a material and its environment and is, therefore, highly suited to study by atomistic modeling techniques. In this paper, the complex nature of corrosion processes and mechanisms is briefly reviewed. Various atomistic methods for exploring corrosion mechanisms are then described, and recent applications in the literature surveyed. Several instances of the application of atomistic modeling to corrosion science are then reviewed in detail, including studies of the metal-water interface, the reaction of water on electrified metallic interfaces, the dissolution of metal atoms from metallic surfaces, and the role of competitive adsorption in controlling the chemical nature and structure of a metallic surface. Some perspectives are then given concerning the future of atomistic modeling in the field of corrosion science.

Components for Atomistic-to-Continuum Multiscale Modeling of Flow in Micro- and Nanofluidic Systems

Directory of Open Access Journals (Sweden)

Helgi Adalsteinsson

2008-01-01

Full Text Available Micro- and nanofluidics pose a series of significant challenges for science-based modeling. Key among those are the wide separation of length- and timescales between interface phenomena and bulk flow and the spatially heterogeneous solution properties near solid-liquid interfaces. It is not uncommon for characteristic scales in these systems to span nine orders of magnitude from the atomic motions in particle dynamics up to evolution of mass transport at the macroscale level, making explicit particle models intractable for all but the simplest systems. Recently, atomistic-to-continuum (A2C multiscale simulations have gained a lot of interest as an approach to rigorously handle particle-level dynamics while also tracking evolution of large-scale macroscale behavior. While these methods are clearly not applicable to all classes of simulations, they are finding traction in systems in which tight-binding, and physically important, dynamics at system interfaces have complex effects on the slower-evolving large-scale evolution of the surrounding medium. These conditions allow decomposition of the simulation into discrete domains, either spatially or temporally. In this paper, we describe how features of domain decomposed simulation systems can be harnessed to yield flexible and efficient software for multiscale simulations of electric field-driven micro- and nanofluidics.

Redox reactions with empirical potentials: Atomistic battery discharge simulations

OpenAIRE

Dapp, Wolf B.; Müser, Martin H.

2013-01-01

Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each ...

Simulating the Physical World

Science.gov (United States)

Berendsen, Herman J. C.

2004-06-01

The simulation of physical systems requires a simplified, hierarchical approach which models each level from the atomistic to the macroscopic scale. From quantum mechanics to fluid dynamics, this book systematically treats the broad scope of computer modeling and simulations, describing the fundamental theory behind each level of approximation. Berendsen evaluates each stage in relation to its applications giving the reader insight into the possibilities and limitations of the models. Practical guidance for applications and sample programs in Python are provided. With a strong emphasis on molecular models in chemistry and biochemistry, this book will be suitable for advanced undergraduate and graduate courses on molecular modeling and simulation within physics, biophysics, physical chemistry and materials science. It will also be a useful reference to all those working in the field. Additional resources for this title including solutions for instructors and programs are available online at www.cambridge.org/9780521835275. The first book to cover the wide range of modeling and simulations, from atomistic to the macroscopic scale, in a systematic fashion Providing a wealth of background material, it does not assume advanced knowledge and is eminently suitable for course use Contains practical examples and sample programs in Python

Atomistic simulation of CO 2 solubility in poly(ethylene oxide) oligomers

KAUST Repository

Hong, Bingbing

2013-10-02

We have performed atomistic molecular dynamics simulations coupled with thermodynamic integration to obtain the excess chemical potential and pressure-composition phase diagrams for CO2 in poly(ethylene oxide) oligomers. Poly(ethylene oxide) dimethyl ether, CH3O(CH 2CH2O)nCH3 (PEO for short) is a widely applied physical solvent that forms the major organic constituent of a class of novel nanoparticle-based absorbents. Good predictions were obtained for pressure-composition-density relations for CO2 + PEO oligomers (2 ≤ n ≤ 12), using the Potoff force field for PEO [J. Chem. Phys. 136, 044514 (2012)] together with the TraPPE model for CO2 [AIChE J. 47, 1676 (2001)]. Water effects on Henrys constant of CO2 in PEO have also been investigated. Addition of modest amounts of water in PEO produces a relatively small increase in Henrys constant. Dependence of the calculated Henrys constant on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. © 2013 Taylor & Francis.

Drug design: Insights from atomistic simulations

International Nuclear Information System (INIS)

Collu, F.; Spiga, E.; Kumar, A.; Hajjar, E.; Vargiu, A.V.; Ceccarelli, M.; Ruggerone, P.

2009-01-01

Computer simulations have become a widely used and powerful tool to study the behaviour of many-particle and many-interaction systems and processes such as nucleic acid dynamics, drug-DNA interactions, enzymatic processes, membrane, antibiotics. The increased reliability of computational techniques has made possible to plane a bottom-up approach in drug design, i.e. designing molecules with improved properties starting from the knowledge of the molecular mechanisms. However, the in silico techniques have to face the fact that the number of degrees of freedom involved in biological systems is very large while the time scale of several biological processes is not accessible to standard simulations. Algorithms and methods have been developed and are still under construction to bridge these gaps. Here we review the activities of our group focussed on the time-scale bottleneck and, in particular, on the use of the meta dynamics scheme that allows the investigation of rare events in reasonable computer time without reducing the accuracy of the calculation. In particular, we have devoted particular attention to the characterization at microscopic level of translocation of antibiotics through membrane pores, aiming at the identification of structural and dynamical features helpful for a rational drug design.

Atomistic modeling of carbon Cottrell atmospheres in bcc iron

Science.gov (United States)

Veiga, R. G. A.; Perez, M.; Becquart, C. S.; Domain, C.

2013-01-01

Atomistic simulations with an EAM interatomic potential were used to evaluate carbon-dislocation binding energies in bcc iron. These binding energies were then used to calculate the occupation probability of interstitial sites in the vicinity of an edge and a screw dislocation. The saturation concentration due to carbon-carbon interactions was also estimated by atomistic simulations in the dislocation core and taken as an upper limit for carbon concentration in a Cottrell atmosphere. We obtained a maximum concentration of 10 ± 1 at.% C at T = 0 K within a radius of 1 nm from the dislocation lines. The spatial carbon distributions around the line defects revealed that the Cottrell atmosphere associated with an edge dislocation is denser than that around a screw dislocation, in contrast with the predictions of the classical model of Cochardt and colleagues. Moreover, the present Cottrell atmosphere model is in reasonable quantitative accord with the three-dimensional atom probe data available in the literature.

Discrete simulations of spatio-temporal dynamics of small water bodies under varied stream flow discharges

Science.gov (United States)

Daya Sagar, B. S.

2005-01-01

Spatio-temporal patterns of small water bodies (SWBs) under the influence of temporally varied stream flow discharge are simulated in discrete space by employing geomorphologically realistic expansion and contraction transformations. Cascades of expansion-contraction are systematically performed by synchronizing them with stream flow discharge simulated via the logistic map. Templates with definite characteristic information are defined from stream flow discharge pattern as the basis to model the spatio-temporal organization of randomly situated surface water bodies of various sizes and shapes. These spatio-temporal patterns under varied parameters (λs) controlling stream flow discharge patterns are characterized by estimating their fractal dimensions. At various λs, nonlinear control parameters, we show the union of boundaries of water bodies that traverse the water body and non-water body spaces as geomorphic attractors. The computed fractal dimensions of these attractors are 1.58, 1.53, 1.78, 1.76, 1.84, and 1.90, respectively, at λs of 1, 2, 3, 3.46, 3.57, and 3.99. These values are in line with general visual observations.

Discrete simulations of spatio-temporal dynamics of small water bodies under varied stream flow discharges

Directory of Open Access Journals (Sweden)

B. S. Daya Sagar

2005-01-01

Full Text Available Spatio-temporal patterns of small water bodies (SWBs under the influence of temporally varied stream flow discharge are simulated in discrete space by employing geomorphologically realistic expansion and contraction transformations. Cascades of expansion-contraction are systematically performed by synchronizing them with stream flow discharge simulated via the logistic map. Templates with definite characteristic information are defined from stream flow discharge pattern as the basis to model the spatio-temporal organization of randomly situated surface water bodies of various sizes and shapes. These spatio-temporal patterns under varied parameters (λs controlling stream flow discharge patterns are characterized by estimating their fractal dimensions. At various λs, nonlinear control parameters, we show the union of boundaries of water bodies that traverse the water body and non-water body spaces as geomorphic attractors. The computed fractal dimensions of these attractors are 1.58, 1.53, 1.78, 1.76, 1.84, and 1.90, respectively, at λs of 1, 2, 3, 3.46, 3.57, and 3.99. These values are in line with general visual observations.

Atomistic simulations of the yielding of gold nanowires

International Nuclear Information System (INIS)

Diao Jiankuai; Gall, Ken; Dunn, Martin L.; Zimmerman, Jonathan A.

2006-01-01

We performed atomistic simulations to study the effect of free surfaces on the yielding of gold nanowires. Tensile surface stresses on the surfaces of the nanowires cause them to contract along the length with respect to the bulk face-centered cubic lattice and induce compressive stress in the interior. When the cross-sectional area of a nanowire is less than 2.45 nm x 2.45 nm, the wire yields under its surface stresses. Under external forces and surface stresses, nanowires yield via the nucleation and propagation of the {1 1 1} partial dislocations. The magnitudes of the tensile and compressive yield stress of nanowires increase and decrease, respectively, with a decrease of the wire width. The magnitude of the tensile yield stress is much larger than that of the compressive yield stress for small nanowires, while for small nanowires, tensile and compressive yield stresses have similar magnitudes. The critical resolved shear stress (RSS) by external forces depends on wire width, orientation and loading condition (tension vs. compression). However, the critical RSS in the interior of the nanowires, which is exerted by both the external force and the surface-stress-induced compressive stress, does not change significantly with wire width for same orientation and same loading condition, and can thus serve as a 'local' criterion. This local criterion is invoked to explain the observed size dependence of yield behavior and tensile/compressive yield stress asymmetry, considering surface stress effects and different slip systems active in tensile and compressive yielding

Long time scale simulation of a grain boundary in copper

DEFF Research Database (Denmark)

Pedersen, A.; Henkelman, G.; Schiøtz, Jakob

2009-01-01

A general, twisted and tilted, grain boundary in copper has been simulated using the adaptive kinetic Monte Carlo method to study the atomistic structure of the non-crystalline region and the mechanism of annealing events that occur at low temperature. The simulated time interval spanned 67 mu s...... was also observed. In the final low-energy configurations, the thickness of the region separating the crystalline grains corresponds to just one atomic layer, in good agreement with reported experimental observations. The simulated system consists of 1307 atoms and atomic interactions were described using...

Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations

DEFF Research Database (Denmark)

Franova, M. D.; Vattulainen, I.; Ollila, O. H. S.

2014-01-01

The lateral pressure profile of lipid bilayers has gained a lot of attention, since changes in the pressure profile have been suggested to shift the membrane protein conformational equilibrium. This relation has been mostly studied with theoretical methods, especially with molecular dynamics....../monomer fluorescence ratio has been assumed to represent the lateral pressure in the location of the pyrene moieties. Here, we consider the validity of this assumption through atomistic molecular dynamics simulations in a DOPC (dioleoylphosphatidylcholine) membrane, which hosts di-pyr-PC probes with different acyl...... simulations, since established methods to measure the lateral pressure profile experimentally have not been available. The only experiments that have attempted to gauge the lateral pressure profile have been done by using di-pyrenyl-phosphatidylcholine (di-pyr-PC) probes. In these experiments, the excimer...

Multi-Scale Modelling of Deformation and Fracture in a Biomimetic Apatite-Protein Composite: Molecular-Scale Processes Lead to Resilience at the μm-Scale.

Directory of Open Access Journals (Sweden)

Dirk Zahn

Full Text Available Fracture mechanisms of an enamel-like hydroxyapatite-collagen composite model are elaborated by means of molecular and coarse-grained dynamics simulation. Using fully atomistic models, we uncover molecular-scale plastic deformation and fracture processes initiated at the organic-inorganic interface. Furthermore, coarse-grained models are developed to investigate fracture patterns at the μm-scale. At the meso-scale, micro-fractures are shown to reduce local stress and thus prevent material failure after loading beyond the elastic limit. On the basis of our multi-scale simulation approach, we provide a molecular scale rationalization of this phenomenon, which seems key to the resilience of hierarchical biominerals, including teeth and bone.

Spatio-temporal modelling of atmospheric pollution based on observations provided by an air quality monitoring network at a regional scale

International Nuclear Information System (INIS)

Coman, A.

2008-01-01

This study is devoted to the spatio-temporal modelling of air pollution at a regional scale using a set of statistical methods in order to treat the measurements of pollutant concentrations (NO 2 , O 3 ) provided by an air quality monitoring network (AIRPARIF). The main objective is the improvement of the pollutant fields mapping using either interpolation methods based on the spatial or spatio-temporal structure of the data (spatial or spatio-temporal kriging) or some algorithms taking into account the observations, in order to correct the concentrations simulated by a deterministic model (Ensemble Kalman Filter). The results show that nitrogen dioxide mapping based only on spatial interpolation (kriging) gives the best results, while the spatial repartition of the monitoring sites is good. For the ozone mapping it is the sequential data assimilation that leads us to a better reconstruction of the plume's form and position for the analyzed cases. Complementary to the pollutant mapping, another objective was to perform a local prediction of ozone concentrations on a 24-hour horizon; this task was performed using Artificial Neural Networks. The performance indices obtained using two types of neural architectures indicate a fair accuracy especially for the first 8 hours of prediction horizon. (author)

Molecular cooperativity and compatibility via full atomistic simulation

Science.gov (United States)

Kwan Yang, Kenny

Civil engineering has customarily focused on problems from a large-scale perspective, encompassing structures such as bridges, dams, and infrastructure. However, present day challenges in conjunction with advances in nanotechnology have forced a re-focusing of expertise. The use of atomistic and molecular approaches to study material systems opens the door to significantly improve material properties. The understanding that material systems themselves are structures, where their assemblies can dictate design capacities and failure modes makes this problem well suited for those who possess expertise in structural engineering. At the same time, a focus has been given to the performance metrics of materials at the nanoscale, including strength, toughness, and transport properties (e.g., electrical, thermal). Little effort has been made in the systematic characterization of system compatibility -- e.g., how to make disparate material building blocks behave in unison. This research attempts to develop bottom-up molecular scale understanding of material behavior, with the global objective being the application of this understanding into material design/characterization at an ultimate functional scale. In particular, it addresses the subject of cooperativity at the nano-scale. This research aims to define the conditions which dictate when discrete molecules may behave as a single, functional unit, thereby facilitating homogenization and up-scaling approaches, setting bounds for assembly, and providing a transferable assessment tool across molecular systems. Following a macro-scale pattern where the compatibility of deformation plays a vital role in the structural design, novel geometrical cooperativity metrics based on the gyration tensor are derived with the intention to define nano-cooperativity in a generalized way. The metrics objectively describe the general size, shape and orientation of the structure. To validate the derived measures, a pair of ideal macromolecules

From beta-relaxation to alpha-decay: Atomistic picture from molecular dynamics simulations for glass-forming Ni0.5Zr0.5 melt

Energy Technology Data Exchange (ETDEWEB)

Teichler, Helmar [Inst. Materialphysik, Univ Goettingen (Germany)

2013-07-01

In glass-forming melts the decay of structural fluctuation shows the well known transition from beta-relaxation (von-Schweidler law with exponent b) to alpha-decay (KWW law with exponent beta). Here we present results from molecular dynamics simulations for a metallic glass forming Ni0.5Zr0.5 model aimed at giving an understanding of this transition on the atomistic scale. At the considered temperature below mode coupling Tc, the dynamics of the system can be interpreted by residence of the particles in their neighbour cages and escape from the cages as rare processes. Our analysis yields that the fraction of residing particles is characterized by a hierarchical law in time, with von-Schweidler b explicitly related to the exponent of this law. In the alpha-decay regime the stretching exponent reflects, in addition, floating of the cages due to strain effects of escaped particles. Accordingly, the change from beta-relaxation to alpha-decay indicates the transition from low to large fraction of escaped particles.

Multiscale modelling of precipitation in concentrated alloys: from atomistic Monte Carlo simulations to cluster dynamics I thermodynamics

Science.gov (United States)

Lépinoux, J.; Sigli, C.

2018-01-01

In a recent paper, the authors showed how the clusters free energies are constrained by the coagulation probability, and explained various anomalies observed during the precipitation kinetics in concentrated alloys. This coagulation probability appeared to be a too complex function to be accurately predicted knowing only the cluster distribution in Cluster Dynamics (CD). Using atomistic Monte Carlo (MC) simulations, it is shown that during a transformation at constant temperature, after a short transient regime, the transformation occurs at quasi-equilibrium. It is proposed to use MC simulations until the system quasi-equilibrates then to switch to CD which is mean field but not limited by a box size like MC. In this paper, we explain how to take into account the information available before the quasi-equilibrium state to establish guidelines to safely predict the cluster free energies.

AACSD: An atomistic analyzer for crystal structure and defects

Science.gov (United States)

Liu, Z. R.; Zhang, R. F.

2018-01-01

We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

Prediction of irradiation induced microstructures in the AgCu model alloy using a multiscale method coupling atomistic and phase field modelling

OpenAIRE

Demange, Gilles; Pontikis, Vassilis; Lunéville, Laurence; Simeone, David

2016-01-01

In this work, a multiscale approach based on phase field was developed to simulate the microstructure's evolution under irradiation in binary systems, from atomic to microstructural scale. For that purpose, an efficient numerical scheme was developed. In the case of AgCu alloy under Krypton ions irradiation, phenomenological parameters were computed using atomistic methods, as a function of the temperature and the irradiation flux. As a result, we predicted the influence of the irradiation fl...

Adaptive spacetime method using Riemann jump conditions for coupled atomistic-continuum dynamics

International Nuclear Information System (INIS)

Kraczek, B.; Miller, S.T.; Haber, R.B.; Johnson, D.D.

2010-01-01

We combine the Spacetime Discontinuous Galerkin (SDG) method for elastodynamics with the mathematically consistent Atomistic Discontinuous Galerkin (ADG) method in a new scheme that concurrently couples continuum and atomistic models of dynamic response in solids. The formulation couples non-overlapping continuum and atomistic models across sharp interfaces by weakly enforcing jump conditions, for both momentum balance and kinematic compatibility, using Riemann values to preserve the characteristic structure of the underlying hyperbolic system. Momentum balances to within machine-precision accuracy over every element, on each atom, and over the coupled system, with small, controllable energy dissipation in the continuum region that ensures numerical stability. When implemented on suitable unstructured spacetime grids, the continuum SDG model offers linear computational complexity in the number of elements and powerful adaptive analysis capabilities that readily bridge between atomic and continuum scales in both space and time. A special trace operator for the atomic velocities and an associated atomistic traction field enter the jump conditions at the coupling interface. The trace operator depends on parameters that specify, at the scale of the atomic spacing, the position of the coupling interface relative to the atoms. In a key finding, we demonstrate that optimizing these parameters suppresses spurious reflections at the coupling interface without the use of non-physical damping or special boundary conditions. We formulate the implicit SDG-ADG coupling scheme in up to three spatial dimensions, and describe an efficient iterative solution scheme that outperforms common explicit schemes, such as the Velocity Verlet integrator. Numerical examples, in 1dxtime and employing both linear and nonlinear potentials, demonstrate the performance of the SDG-ADG method and show how adaptive spacetime meshing reconciles disparate time steps and resolves atomic-scale signals in

How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations

DEFF Research Database (Denmark)

Aijanen, T.; Koivuniemi, A.; Javanainen, M.

2014-01-01

Cholesteryl ester transfer protein (CETP) mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides) and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity...... and thereby raise high density lipoprotein (HDL)-cholesterol and decrease low density lipoprotein (LDL)-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics...... simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site...

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

NARCIS (Netherlands)

Zavadlav, J.; Podgornik, R.; Melo, M.n.; Marrink, S.j.; Praprotnik, M.

2016-01-01

We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell

Dislocations and elementary processes of plasticity in FCC metals: atomic scale simulations; Dislocations et processus elementaires de la plasticite dans les metaux CFC: apports des simulations a l'echelle atomique

Energy Technology Data Exchange (ETDEWEB)

Rodney, D

2000-07-01

We present atomic-scale simulations of two elementary processes of FCC crystal plasticity. The first study consists in the simulation by molecular dynamics, in a nickel crystal, of the interactions between an edge dislocation and glissile interstitial loops of the type that form under irradiation in displacement cascades. The simulations show various atomic-scale interaction processes leading to the absorption and drag of the loops by the dislocation. These reactions certainly contribute to the formation of the 'clear bands' observed in deformed irradiated materials. The simulations also allow to study quantitatively the role of the glissile loops in irradiation hardening. In particular, dislocation unpinning stresses for certain pinning mechanisms are evaluated from the simulations. The second study consists first in the generalization in three dimensions of the quasi-continuum method (QCM), a multi-scale simulation method which couples atomistic techniques and the finite element method. In the QCM, regions close to dislocation cores are simulated at the atomic-scale while the rest of the crystal is simulated with a lower resolution by means of a discretization of the displacement fields using the finite element method. The QCM is then tested on the simulation of the formation and breaking of dislocation junctions in an aluminum crystal. Comparison of the simulations with an elastic model of dislocation junctions shows that the structure and strength of the junctions are dominated by elastic line tension effects, as is assumed in classical theories. (author)

Atomistic k ⋅ p theory

Energy Technology Data Exchange (ETDEWEB)

Pryor, Craig E., E-mail: craig-pryor@uiowa.edu [Department of Physics and Astronomy, University of Iowa, Iowa City, Iowa 52242 (United States); Pistol, M.-E., E-mail: mats-erik.pistol@ftf.lth.se [NanoLund and Solid State Physics, Lund University, P.O. Box 118, 221 00 Lund (Sweden)

2015-12-14

Pseudopotentials, tight-binding models, and k ⋅ p theory have stood for many years as the standard techniques for computing electronic states in crystalline solids. Here, we present the first new method in decades, which we call atomistic k ⋅ p theory. In its usual formulation, k ⋅ p theory has the advantage of depending on parameters that are directly related to experimentally measured quantities, however, it is insensitive to the locations of individual atoms. We construct an atomistic k ⋅ p theory by defining envelope functions on a grid matching the crystal lattice. The model parameters are matrix elements which are obtained from experimental results or ab initio wave functions in a simple way. This is in contrast to the other atomistic approaches in which parameters are fit to reproduce a desired dispersion and are not expressible in terms of fundamental quantities. This fitting is often very difficult. We illustrate our method by constructing a four-band atomistic model for a diamond/zincblende crystal and show that it is equivalent to the sp{sup 3} tight-binding model. We can thus directly derive the parameters in the sp{sup 3} tight-binding model from experimental data. We then take the atomistic limit of the widely used eight-band Kane model and compute the band structures for all III–V semiconductors not containing nitrogen or boron using parameters fit to experimental data. Our new approach extends k ⋅ p theory to problems in which atomistic precision is required, such as impurities, alloys, polytypes, and interfaces. It also provides a new approach to multiscale modeling by allowing continuum and atomistic k ⋅ p models to be combined in the same system.

Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations

DEFF Research Database (Denmark)

Koivuniemi, A.; Vuorela, T.; Kovanen, P. T.

2012-01-01

molecular dynamics simulations to unravel the mechanisms associated with the CETP-mediated lipid exchange. To this end we used both atomistic and coarse-grained models whose results were consistent with each other. We found CETP to bind to the surface of high density lipoprotein (HDL) -like lipid droplets......Cholesteryl ester transfer protein (CETP) transports cholesteryl esters, triglycerides, and phospholipids between different lipoprotein fractions in blood plasma. The inhibition of CETP has been shown to be a sound strategy to prevent and treat the development of coronary heart disease. We employed...... evidence that helix X acts as a lid which conducts lipid exchange by alternating the open and closed states. The findings have potential for the design of novel molecular agents to inhibit the activity of CETP....

Atomistic modeling of BN nanofillers for mechanical and thermal properties: a review.

Science.gov (United States)

Kumar, Rajesh; Parashar, Avinash

2016-01-07

Due to their exceptional mechanical properties, thermal conductivity and a wide band gap (5-6 eV), boron nitride nanotubes and nanosheets have promising applications in the field of engineering and biomedical science. Accurate modeling of failure or fracture in a nanomaterial inherently involves coupling of atomic domains of cracks and voids as well as a deformation mechanism originating from grain boundaries. This review highlights the recent progress made in the atomistic modeling of boron nitride nanofillers. Continuous improvements in computational power have made it possible to study the structural properties of these nanofillers at the atomistic scale.

Spatiotemporal Simulation of Tourist Town Growth Based on the Cellular Automata Model: The Case of Sanpo Town in Hebei Province

Directory of Open Access Journals (Sweden)

Jun Yang

2013-01-01

Full Text Available Spatiotemporal simulation of tourist town growth is important for research on land use/cover change under the influence of urbanization. Many scholars have shown great interest in the unique pattern of driving urban development with tourism development. Based on the cellular automata (CA model, we simulated and predicted the spatiotemporal growth of Sanpo town in Hebei Province, using the tourism urbanization growth model. Results showed that (1 average annual growth rate of the entire region was 1.5 Ha2 per year from 2005 to 2010, 4 Ha2 per year from 2010 to 2015, and 2.5 Ha2 per year from 2015 to 2020; (2 urban growth rate increased yearly, with regional differences, and had a high degree of correlation with the Euclidean distance of town center, traffic route, attractions, and other factors; (3 Gougezhuang, an important village center in the west of the town, demonstrated traffic advantages and increased growth rate since 2010; (4 Magezhuang village has the largest population in the region, so economic advantages have driven the development of rural urbanization. It showed that CA had high reliability in simulating the spatiotemporal evolution of tourist town, which assists the study of spatiotemporal growth under urbanization and rational protection of tourism resources.

Multi-scale modeling of inter-granular fracture in UO2

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, Pritam [Idaho National Lab. (INL), Idaho Falls, ID (United States); Zhang, Yongfeng [Idaho National Lab. (INL), Idaho Falls, ID (United States); Tonks, Michael R. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Biner, S. Bulent [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2015-03-01

A hierarchical multi-scale approach is pursued in this work to investigate the influence of porosity, pore and grain size on the intergranular brittle fracture in UO2. In this approach, molecular dynamics simulations are performed to obtain the fracture properties for different grain boundary types. A phase-field model is then utilized to perform intergranular fracture simulations of representative microstructures with different porosities, pore and grain sizes. In these simulations the grain boundary fracture properties obtained from molecular dynamics simulations are used. The responses from the phase-field fracture simulations are then fitted with a stress-based brittle fracture model usable at the engineering scale. This approach encapsulates three different length and time scales, and allows the development of microstructurally informed engineering scale model from properties evaluated at the atomistic scale.

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology

Directory of Open Access Journals (Sweden)

Gerber Susanne

2011-04-01

Full Text Available Abstract Background Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. Results The Spatio-Temporal Simulation Environment (STSE is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images. STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.

Science.gov (United States)

Stoma, Szymon; Fröhlich, Martina; Gerber, Susanne; Klipp, Edda

2011-04-28

Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. The Spatio-Temporal Simulation Environment (STSE) is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI) tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images). STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS) and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts of the STSE design and workflow. We

Coupling Strategies Investigation of Hybrid Atomistic-Continuum Method Based on State Variable Coupling

Directory of Open Access Journals (Sweden)

Qian Wang

2017-01-01

Full Text Available Different configurations of coupling strategies influence greatly the accuracy and convergence of the simulation results in the hybrid atomistic-continuum method. This study aims to quantitatively investigate this effect and offer the guidance on how to choose the proper configuration of coupling strategies in the hybrid atomistic-continuum method. We first propose a hybrid molecular dynamics- (MD- continuum solver in LAMMPS and OpenFOAM that exchanges state variables between the atomistic region and the continuum region and evaluate different configurations of coupling strategies using the sudden start Couette flow, aiming to find the preferable configuration that delivers better accuracy and efficiency. The major findings are as follows: (1 the C→A region plays the most important role in the overlap region and the “4-layer-1” combination achieves the best precision with a fixed width of the overlap region; (2 the data exchanging operation only needs a few sampling points closer to the occasions of interactions and decreasing the coupling exchange operations can reduce the computational load with acceptable errors; (3 the nonperiodic boundary force model with a smoothing parameter of 0.1 and a finer parameter of 20 can not only achieve the minimum disturbance near the MD-continuum interface but also keep the simulation precision.

Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys

International Nuclear Information System (INIS)

Djurabekova, F.G.; Domingos, R.; Cerchiara, G.; Castin, N.; Vincent, E.; Malerba, L.

2007-01-01

Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed

Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys

Energy Technology Data Exchange (ETDEWEB)

Djurabekova, F.G. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Domingos, R. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Cerchiara, G. [Department of Nuclear and Production Engineering, University of Pisa (Italy); Castin, N. [Catholic University of Louvain-la-Neuve (Belgium); Vincent, E. [LMPGM UMR-8517, University of Lille I, Villeneuve d' Ascq (France); Malerba, L. [Reactor Materials Research Unit, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium)]. E-mail: lmalerba@sckcen.be

2007-02-15

Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed.

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

International Nuclear Information System (INIS)

Fogarty, Aoife C.; Potestio, Raffaello; Kremer, Kurt

2015-01-01

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

Energy Technology Data Exchange (ETDEWEB)

Fogarty, Aoife C., E-mail: fogarty@mpip-mainz.mpg.de; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de; Kremer, Kurt, E-mail: kremer@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)

2015-05-21

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

Atomistic modeling of dropwise condensation

Energy Technology Data Exchange (ETDEWEB)

Sikarwar, B. S., E-mail: bssikarwar@amity.edu; Singh, P. L. [Department of Mechanical Engineering, Amity University Uttar Pradesh, Noida (India); Muralidhar, K.; Khandekar, S. [Department of Mechanical Engineering, IIT Kanpur (India)

2016-05-23

The basic aim of the atomistic modeling of condensation of water is to determine the size of the stable cluster and connect phenomena occurring at atomic scale to the macroscale. In this paper, a population balance model is described in terms of the rate equations to obtain the number density distribution of the resulting clusters. The residence time is taken to be large enough so that sufficient time is available for all the adatoms existing in vapor-phase to loose their latent heat and get condensed. The simulation assumes clusters of a given size to be formed from clusters of smaller sizes, but not by the disintegration of the larger clusters. The largest stable cluster size in the number density distribution is taken to be representative of the minimum drop radius formed in a dropwise condensation process. A numerical confirmation of this result against predictions based on a thermodynamic model has been obtained. Results show that the number density distribution is sensitive to the surface diffusion coefficient and the rate of vapor flux impinging on the substrate. The minimum drop radius increases with the diffusion coefficient and the impinging vapor flux; however, the dependence is weak. The minimum drop radius predicted from thermodynamic considerations matches the prediction of the cluster model, though the former does not take into account the effect of the surface properties on the nucleation phenomena. For a chemically passive surface, the diffusion coefficient and the residence time are dependent on the surface texture via the coefficient of friction. Thus, physical texturing provides a means of changing, within limits, the minimum drop radius. The study reveals that surface texturing at the scale of the minimum drop radius does not provide controllability of the macro-scale dropwise condensation at large timescales when a dynamic steady-state is reached.

Simulation of the optical coating deposition

Science.gov (United States)

Grigoriev, Fedor; Sulimov, Vladimir; Tikhonravov, Alexander

2018-04-01

A brief review of the mathematical methods of thin-film growth simulation and results of their applications is presented. Both full-atomistic and multi-scale approaches that were used in the studies of thin-film deposition are considered. The results of the structural parameter simulation including density profiles, roughness, porosity, point defect concentration, and others are discussed. The application of the quantum level methods to the simulation of the thin-film electronic and optical properties is considered. Special attention is paid to the simulation of the silicon dioxide thin films.

A FRAMEWORK FOR ONLINE SPATIO-TEMPORAL DATA VISUALIZATION BASED ON HTML5

Directory of Open Access Journals (Sweden)

B. Mao

2012-07-01

Full Text Available Web is entering a new phase – HTML5. New features of HTML5 should be studied for online spatio-temporal data visualization. In the proposed framework, spatio-temporal data is stored in the data server and is sent to user browsers with WebSocket. Public geo-data such as Internet digital map is integrated into the browsers. Then animation is implemented through the canvas object defined by the HTML5 specification. To simulate the spatio-temporal data source, we collected the daily location of 15 users with GPS tracker. The current positions of the users are collected every minute and are recorded in a file. Based on this file, we generate a real time spatio-temporal data source which sends out current user location every second.By enlarging the real time scales by 60 times, we can observe the movement clearly. The data transmitted with WebSocket is the coordinates of users' current positions, which will can be demonstrated in client browsers.

Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex.

Directory of Open Access Journals (Sweden)

Yunqiang Bian

2014-04-01

Full Text Available In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and K(+ ions explicitly modeled. Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations, the free energy landscape of this G-DNA was obtained for the first time and four folding intermediates were identified, including a triplex and a basically formed quadruplex. The simulations also provided atomistic pictures for the structures and cation binding patterns of the intermediates. The results showed that the structure formation and cation binding are cooperative and mutually supporting each other. The syn/anti reorientation dynamics of the intermediates was also investigated. It was found that the nucleotides usually take correct syn/anti configurations when they form native and stable hydrogen bonds with the others, while fluctuating between two configurations when they do not. Misfolded intermediates with wrong syn/anti configurations were observed in the early intermediates but not in the later ones. Based on the simulations, we also discussed the roles of the non-native interactions. Besides, the formation process of the parallel conformation in the first two G-repeats and the associated reversal loop were studied. Based on the above results, we proposed a folding pathway for the hybrid-1 type G-quadruplex with atomistic details, which is new and more complete compared with previous ones. The knowledge gained for this type of G-DNA may provide a general insight for the folding of the other G-quadruplexes.

Uncertainty assessment of PM2.5 contamination mapping using spatiotemporal sequential indicator simulations and multi-temporal monitoring data

Science.gov (United States)

Yang, Yong; Christakos, George; Huang, Wei; Lin, Chengda; Fu, Peihong; Mei, Yang

2016-04-01

Because of the rapid economic growth in China, many regions are subjected to severe particulate matter pollution. Thus, improving the methods of determining the spatiotemporal distribution and uncertainty of air pollution can provide considerable benefits when developing risk assessments and environmental policies. The uncertainty assessment methods currently in use include the sequential indicator simulation (SIS) and indicator kriging techniques. However, these methods cannot be employed to assess multi-temporal data. In this work, a spatiotemporal sequential indicator simulation (STSIS) based on a non-separable spatiotemporal semivariogram model was used to assimilate multi-temporal data in the mapping and uncertainty assessment of PM2.5 distributions in a contaminated atmosphere. PM2.5 concentrations recorded throughout 2014 in Shandong Province, China were used as the experimental dataset. Based on the number of STSIS procedures, we assessed various types of mapping uncertainties, including single-location uncertainties over one day and multiple days and multi-location uncertainties over one day and multiple days. A comparison of the STSIS technique with the SIS technique indicate that a better performance was obtained with the STSIS method.

Spatio-Temporal Simulation and Analysis of Regional Ecological Security Based on Lstm

Science.gov (United States)

Gong, C.; Qi, L.; Heming, L.; Karimian, H.; Yuqin, M.

2017-10-01

Region is a complicated system, where human, nature and society interact and influence. Quantitative modeling and simulation of ecology in the region are the key to realize the strategy of regional sustainable development. Traditional machine learning methods have made some achievements in the modeling of regional ecosystems, but it is difficult to determine the learning characteristics and to realize spatio-temporal simulation. Deep learning does not need prior identification of training characteristics, have excellent feature learning ability, can improve the accuracy of model prediction, so the use of deep learning model has a significant advantage. Therefore, we use net primary productivity (NPP), atmospheric optical depth (AOD), moderate-resolution imaging spectrometer (MODIS), Normalized Difference Vegetation Index (NDVI), landcover and population data, and use LSTM to do spatio-temporal simulation. We conduct spatial analysis and driving force analysis. The conclusions are as follows: the ecological deficit of northwestern Henan and urban communities such as Zhengzhou is higher. The reason of former lies in the weak land productivity of the Loess Plateau, the irrational crop cultivation mode. The latter lies in the high consumption of resources in the large urban agglomeration; The positive trend of Henan ecological development from 2013 is mainly due to the effective environmental protection policy in the 12th five-year plan; The main driver of the sustained ecological deficit growth of Henan in 2004-2013 is high-speed urbanization, increasing population and goods consumption. This article provides relevant basic scientific support and reference for the regional ecological scientific management and construction.

SPATIO-TEMPORAL SIMULATION AND ANALYSIS OF REGIONAL ECOLOGICAL SECURITY BASED ON LSTM

Directory of Open Access Journals (Sweden)

C. Gong

2017-10-01

Full Text Available Region is a complicated system, where human, nature and society interact and influence. Quantitative modeling and simulation of ecology in the region are the key to realize the strategy of regional sustainable development. Traditional machine learning methods have made some achievements in the modeling of regional ecosystems, but it is difficult to determine the learning characteristics and to realize spatio-temporal simulation. Deep learning does not need prior identification of training characteristics, have excellent feature learning ability, can improve the accuracy of model prediction, so the use of deep learning model has a significant advantage. Therefore, we use net primary productivity (NPP, atmospheric optical depth (AOD, moderate-resolution imaging spectrometer (MODIS, Normalized Difference Vegetation Index (NDVI, landcover and population data, and use LSTM to do spatio-temporal simulation. We conduct spatial analysis and driving force analysis. The conclusions are as follows: the ecological deficit of northwestern Henan and urban communities such as Zhengzhou is higher. The reason of former lies in the weak land productivity of the Loess Plateau, the irrational crop cultivation mode. The latter lies in the high consumption of resources in the large urban agglomeration; The positive trend of Henan ecological development from 2013 is mainly due to the effective environmental protection policy in the 12th five-year plan; The main driver of the sustained ecological deficit growth of Henan in 2004-2013 is high-speed urbanization, increasing population and goods consumption. This article provides relevant basic scientific support and reference for the regional ecological scientific management and construction.

Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry

DEFF Research Database (Denmark)

Petersen, Michael; Madsen, Jeppe B; Jørgensen, Thomas J D

2017-01-01

activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations...... are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1......Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen...

Key role of water in proton transfer at the Q(o)-site of the cytochrome bc(1) complex predicted by atomistic molecular dynamics simulations

DEFF Research Database (Denmark)

Postila, P. A.; Kaszuba, K.; Sarewicz, M.

2013-01-01

of the cyt bc(1) function have remained unclear especially regarding the substrate binding at the Q(o)-site. In this work we address this issue by performing extensive atomistic molecular dynamics simulations with the cyt bc(1) complex of Rhodobacter capsulatus embedded in a lipid bilayer. Based...... on the simulations we are able to show the atom-level binding modes of two substrate forms: quinol (QH(2)) and quinone (Q). The QH(2) binding at the Q(o)-site involves a coordinated water arrangement that produces an exceptionally close and stable interaction between the cyt b and iron sulfur protein subunits...

Atomistic approach for modeling metal-semiconductor interfaces

DEFF Research Database (Denmark)

Stradi, Daniele; Martinez, Umberto; Blom, Anders

2016-01-01

realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via the I–V curve. In particular, it will be demonstrated how doping — and bias — modifies the Schottky barrier, and how finite size models (the slab approach) are unable to describe these interfaces......We present a general framework for simulating interfaces using an atomistic approach based on density functional theory and non-equilibrium Green's functions. The method includes all the relevant ingredients, such as doping and an accurate value of the semiconductor band gap, required to model...

Study of plasticity in metals by numerical simulations

International Nuclear Information System (INIS)

Clouet, E.

2013-01-01

We present a study of the plastic behaviour in metals based on the modelling of dislocation properties. Different simulation tools have been used and developed to study plasticity in structural materials, in particular metals used in the nuclear industry. In iron or zirconium alloys, plasticity is controlled at low temperature by the glide of screw dislocations. Atomistic simulations can be used to model dislocation core properties and thus to obtain a better knowledge of the mechanisms controlling dislocation glide. Such atomistic simulations need nevertheless some special care because of the long range elastic field induced by the dislocations. We have therefore developed a modelling approach relying both on atomistic simulations, using either empirical interatomic potentials or ab initio calculations, and on elasticity theory. Such an approach has been used to obtain dislocation intrinsic core properties. These simulations allowed us to describe, in iron, the variations of these core properties with the dislocation character. In zirconium, we could identity the origin of the high lattice friction and obtain a better understanding of the competition between the different glide systems. At high temperature, dislocations do not only glide but can also cross-slip or climb. This leads to a motion of the dislocations out of their glide plane which needs to be considered when modelling the plastic flow. We performed a study of dislocation climb at different scales, leading to the implementation of a dislocation climb model in dislocation dynamics simulations. (author) [fr

Crack growth and fracture toughness of amorphous Li-Si anodes: Mechanisms and role of charging/discharging studied by atomistic simulations

Science.gov (United States)

Khosrownejad, S. M.; Curtin, W. A.

2017-10-01

Fracture is the main cause of degradation and capacity fading in lithiated silicon during cycling. Experiments on the fracture of lithiated silicon show conflicting results, and so mechanistic models can help interpret experiments and guide component design. Here, large-scale K-controlled atomistic simulations of crack propagation (R-curve KI vs. Δa) are performed at LixSi compositions x = 0.5 , 1.0 , 1.5 for as-quenched/relaxed samples and at x = 0.5 , 1.0 for samples created by discharging from higher Li compositions. In all cases, the fracture mechanism is void nucleation, growth, and coalescence. In as-quenched materials, with increasing Li content the plastic flow stress and elastic moduli decrease but void nucleation and growth happen at smaller stress, so that the initial fracture toughness KIc ≈ 1.0 MPa√{ m} decreases slightly but the initial fracture energy JIc ≈ 10.5J/m2 is similar. After 10 nm of crack growth, the fracture toughnesses increase and become similar at KIc ≈ 1.9 MPa√{ m} across all compositions. Plane-strain equi-biaxial expansion simulations of uncracked samples provide complementary information on void nucleation and growth. The simulations are interpreted within the framework of Gurson model for ductile fracture, which predicts JIc = ασy D where α ≃ 1 and D is the void spacing, and good agreement is found. In spite of flowing plastically, the fracture toughness of LixSi is low because voids nucleate within nano-sized distances ahead of the crack (D ≈ 1nm). Scaling simulation results to experimental conditions, reasonable agreement with experimentally-estimated fracture toughnesses is obtained. The discharging process facilitates void nucleation but decreases the flow stress (as shown previously), leading to enhanced fracture toughness at all levels of crack growth. Therefore, the fracture behavior of lithiated silicon at a given composition is not a material property but instead depends on the history of charging

Atomistically informed solute drag in Al–Mg

International Nuclear Information System (INIS)

Zhang, F; Curtin, W A

2008-01-01

Solute drag in solute-strengthened alloys, caused by diffusion of solute atoms around moving dislocations, controls the stress at deformation rates and temperatures useful for plastic forming processes. In the technologically important Al–Mg alloys, the solute drag stresses predicted by classical theories are much larger than experiments, which is resolved in general by eliminating the singularity of the dislocation core via Peierls–Nabarro-type models. Here, the drag stress versus dislocation velocity is computed numerically using a realistic dislocation core structure obtained from an atomistic model to investigate the role of the core and obtain quantitative stresses for comparison with experiment. The model solves a discrete diffusion equation in a reference frame moving with the dislocation, with input solute enthalpies and diffusion activation barriers in the core computed by or estimated from atomistic studies. At low dislocation velocities, the solute drag stress is controlled by bulk solute diffusion because the core diffusion occurs too quickly. In this regime, the drag stress can be obtained using a Peierls–Nabarro model with a core spreading parameter tuned to best match the atomistic models. At intermediate velocities, both bulk and core diffusion can contribute to the drag, leading to a complex stress–velocity relationship showing two peaks in stress. At high velocities, the drag stress is controlled solely by diffusion within and across the core. Like the continuum models, the drag stress is nearly linear in solute concentration. The Orowan relationship is used to connect dislocation velocity to deformation strain rate. Accounting for the dependence of mobile dislocation density on stress, the simulations are in good agreement with experiments on Al–Mg alloys over a range of concentrations and temperatures

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

Energy Technology Data Exchange (ETDEWEB)

Gray, Alan [The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom); Harlen, Oliver G. [University of Leeds, Leeds LS2 9JT (United Kingdom); Harris, Sarah A., E-mail: s.a.harris@leeds.ac.uk [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Leeds, Leeds LS2 9JT (United Kingdom); Khalid, Syma; Leung, Yuk Ming [University of Southampton, Southampton SO17 1BJ (United Kingdom); Lonsdale, Richard [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg (Germany); Mulholland, Adrian J. [University of Bristol, Bristol BS8 1TS (United Kingdom); Pearson, Arwen R. [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Hamburg, Hamburg (Germany); Read, Daniel J.; Richardson, Robin A. [University of Leeds, Leeds LS2 9JT (United Kingdom); The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom)

2015-01-01

The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

Science.gov (United States)

Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Kunaseth, Manaschai; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Ohmura, Satoshi; Rajak, Pankaj; Shimamura, Kohei; Vashishta, Priya

2014-05-01

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 106-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

International Nuclear Information System (INIS)

Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya; Kunaseth, Manaschai; Ohmura, Satoshi; Shimamura, Kohei

2014-01-01

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10 6 -atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of

Redox reactions with empirical potentials: atomistic battery discharge simulations.

Science.gov (United States)

Dapp, Wolf B; Müser, Martin H

2013-08-14

Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

Spatio-temporal spectra in the logarithmic layer of wall turbulence: large-eddy simulations and simple models

NARCIS (Netherlands)

Wilczek, Michael; Stevens, Richard Johannes Antonius Maria; Meneveau, Charles

2015-01-01

Motivated by the need to characterize the spatio-temporal structure of turbulence in wall-bounded flows, we study wavenumber–frequency spectra of the streamwise velocity component based on large-eddy simulation (LES) data. The LES data are used to measure spectra as a function of the two

Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity

Directory of Open Access Journals (Sweden)

Elena ePapaleo

2015-05-01

Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

Science.gov (United States)

Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

2015-01-01

Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

Parallel multiscale simulations of a brain aneurysm

Energy Technology Data Exchange (ETDEWEB)

Grinberg, Leopold [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States); Fedosov, Dmitry A. [Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich 52425 (Germany); Karniadakis, George Em, E-mail: george_karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States)

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in

Parallel multiscale simulations of a brain aneurysm

International Nuclear Information System (INIS)

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

2013-01-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in

MODELLING AND SIMULATION OF A NEUROPHYSIOLOGICAL EXPERIMENT BY SPATIO-TEMPORAL POINT PROCESSES

Directory of Open Access Journals (Sweden)

Viktor Beneš

2011-05-01

Full Text Available We present a stochastic model of an experimentmonitoring the spiking activity of a place cell of hippocampus of an experimental animal moving in an arena. Doubly stochastic spatio-temporal point process is used to model and quantify overdispersion. Stochastic intensity is modelled by a Lévy based random field while the animal path is simplified to a discrete random walk. In a simulation study first a method suggested previously is used. Then it is shown that a solution of the filtering problem yields the desired inference to the random intensity. Two approaches are suggested and the new one based on finite point process density is applied. Using Markov chain Monte Carlo we obtain numerical results from the simulated model. The methodology is discussed.

Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores

Science.gov (United States)

Yang, Guomin; Neretnieks, Ivars; Holmboe, Michael

2017-08-01

During the last four decades, numerous studies have been directed to the swelling smectite-rich clays in the context of high-level radioactive waste applications and waste-liners for contaminated sites. The swelling properties of clay mineral particles arise due to hydration of the interlayer cations and the diffuse double layers formed near the negatively charged montmorillonite (MMT) surfaces. To accurately study the cation hydration in the interlayer nanopores of MMT, solvent-solute and solvent-clay surface interactions (i.e., the solvation effects and the shape effects) on the atomic level should be taken into account, in contrast to many recent electric double layer based methodologies using continuum models. Therefore, in this research we employed fully atomistic simulations using classical molecular dynamics (MD) simulations, the software package GROMACS along with the CLAYFF forcefield and the SPC/E water model. We present the ion distributions and the deformation of the hydrated coordination structures, i.e., the hydration shells of Na+ and Ca2+ in the interlayer, respectively, for MMT in the first-layer, the second-layer, the third-layer, the fourth-layer, and the fifth-layer (1W, 2W, 3W, 4W, and 5W) hydrate states. Our MD simulations show that Na+ in Na-MMT nanopores have an affinity to the ditrigonal cavities of the clay layers and form transient inner-sphere complexes at about 3.8 Å from clay midplane at water contents less than the 5W hydration state. However, these phenomena are not observed in Ca-MMT regardless of swelling states. For Na-MMT, each Na+ is coordinated to four water molecules and one oxygen atom of the clay basal-plane in the first hydration shell at the 1W hydration state, and with five to six water molecules in the first hydration shell within a radius of 3.1 Å at all higher water contents. In Ca-MMT, however each Ca2+ is coordinated to approximately seven water molecules in the first hydration shell at the 1W hydration state and

Simulating solidification in metals at high pressure: The drive to petascale computing

International Nuclear Information System (INIS)

Streitz, Frederick H; Glosli, James N; Patel, Mehul V; Chan, Bor; Yates, Robert K; Supinski, Bronis R de; Sexton, James; Gunnels, John A

2006-01-01

We investigate solidification in metal systems ranging in size from 64,000 to 524,288,000 atoms on the IBM BlueGene/L computer at LLNL. Using the newly developed ddcMD code, we achieve performance rates as high as 103 TFlops, with a performance of 101.7 TFlop sustained over a 7 hour run on 131,072 cpus. We demonstrate superb strong and weak scaling. Our calculations are significant as they represent the first atomic-scale model of metal solidification to proceed, without finite size effects, from spontaneous nucleation and growth of solid out of the liquid, through the coalescence phase, and into the onset of coarsening. Thus, our simulations represent the first step towards an atomistic model of nucleation and growth that can directly link atomistic to mesoscopic length scales

Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations

DEFF Research Database (Denmark)

Heikkila, E.; Martinez-Seara, H.; Gurtovenko, A. A.

2014-01-01

Despite being chemically inert as a bulk material, nanoscale gold can pose harmful side effects to living organisms. In particular, cationic Au nanoparticles (AuNP+) of 2 nm diameter or less permeate readily through plasma membranes and induce cell death. We report atomistic simulations of cationic...... to be governed by cooperative effects where AuNP+, counterions, water, and the two membrane leaflets all contribute. On the extracellular side, we find that the nanoparticle has to cross a free energy barrier of about 5 k(B)T prior forming a stable contact with the membrane. This results in a rearrangement...

Dislocation climb models from atomistic scheme to dislocation dynamics

OpenAIRE

Niu, Xiaohua; Luo, Tao; Lu, Jianfeng; Xiang, Yang

2016-01-01

We develop a mesoscopic dislocation dynamics model for vacancy-assisted dislocation climb by upscalings from a stochastic model on the atomistic scale. Our models incorporate microscopic mechanisms of (i) bulk diffusion of vacancies, (ii) vacancy exchange dynamics between bulk and dislocation core, (iii) vacancy pipe diffusion along the dislocation core, and (iv) vacancy attachment-detachment kinetics at jogs leading to the motion of jogs. Our mesoscopic model consists of the vacancy bulk dif...

Multiscale methods coupling atomistic and continuum mechanics: analysis of a simple case

OpenAIRE

Blanc , Xavier; Le Bris , Claude; Legoll , Frédéric

2007-01-01

International audience; The description and computation of fine scale localized phenomena arising in a material (during nanoindentation, for instance) is a challenging problem that has given birth to many multiscale methods. In this work, we propose an analysis of a simple one-dimensional method that couples two scales, the atomistic one and the continuum mechanics one. The method includes an adaptive criterion in order to split the computational domain into two subdomains, that are described...

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Science.gov (United States)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations.

Directory of Open Access Journals (Sweden)

Tarja Äijänen

2014-11-01

Full Text Available Cholesteryl ester transfer protein (CETP mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity and thereby raise high density lipoprotein (HDL-cholesterol and decrease low density lipoprotein (LDL-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site of anacetrapib turns out to reside in the tunnel inside CETP, near the residues surrounding the N-terminal opening. Free energy calculations show that when anacetrapib resides in this area, it hinders the ability of cholesteryl ester to diffuse out from CETP. The simulations further bring out the ability of anacetrapib to regulate the structure-function relationships of phospholipids and helix X, the latter representing the structural region of CETP important to the process of neutral lipid exchange with lipoproteins. Altogether, the simulations propose CETP inhibition to be realized when anacetrapib is transferred into the lipid binding pocket. The novel insight gained in this study has potential use in the development of new molecular agents capable of preventing the progression of cardiovascular diseases.

Comparison of atomistic and elasticity approaches for carbon diffusion near line defects in {alpha}-iron

Energy Technology Data Exchange (ETDEWEB)

Veiga, R.G.A., E-mail: rgaveiga@gmail.com [Universite de Lyon, INSA Lyon, Laboratoire MATEIS, UMR CNRS 5510, 25 Avenue Jean Capelle, F69621, Villeurbanne (France); Perez, M. [Universite de Lyon, INSA Lyon, Laboratoire MATEIS, UMR CNRS 5510, 25 Avenue Jean Capelle, F69621, Villeurbanne (France); Becquart, C.S. [Unite Materiaux et Transformations (UMET), Ecole Nationale Superieure de Chimie de Lille, UMR CNRS 8207, Bat. C6, F59655 Villeneuve d' Ascq Cedex (France); Laboratoire commun EDF-CNRS Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France); Clouet, E. [Service de Recherches de Metallurgie Physique, CEA/Saclay, 91191 Gif-sur-Yvette (France); Domain, C. [EDF, Recherche et Developpement, Materiaux et Mecanique des Composants, Les Renardieres, F77250 Moret sur Loing (France); Laboratoire commun EDF-CNRS Etude et Modelisation des Microstructures pour le Vieillissement des Materiaux (EM2VM) (France)

2011-10-15

Energy barriers for carbon migration in the neighborhood of line defects in body-centered cubic iron have been obtained by atomistic simulations. For this purpose, molecular statics with an Fe-C interatomic potential, based on the embedded atom method, has been employed. Results of these simulations have been compared to the predictions of anisotropic elasticity theory. The agreement is better for a carbon atom sitting on an octahedral site (energy minimum) than one on a tetrahedral site (saddle point). Absolute differences in the energy barriers obtained by the two methods are usually below 5 meV at distances larger than 1.5 nm from a screw dislocation and 2 nm (up to 4 nm in the glide plane) from the edge dislocation. Atomistic kinetic Monte Carlo simulations performed at T = 300 K and additional analysis based on the activation energies obtained by both methods show that they are in good qualitative agreement, despite some important quantitative discrepancies due to the large absolute errors found near the dislocation cores.

Crystalline cellulose elastic modulus predicted by atomistic models of uniform deformation and nanoscale indentation

Science.gov (United States)

Xiawa Wu; Robert J. Moon; Ashlie Martini

2013-01-01

The elastic modulus of cellulose Iß in the axial and transverse directions was obtained from atomistic simulations using both the standard uniform deformation approach and a complementary approach based on nanoscale indentation. This allowed comparisons between the methods and closer connectivity to experimental measurement techniques. A reactive...

The Adaptive Multi-scale Simulation Infrastructure

Energy Technology Data Exchange (ETDEWEB)

Tobin, William R. [Rensselaer Polytechnic Inst., Troy, NY (United States)

2015-09-01

The Adaptive Multi-scale Simulation Infrastructure (AMSI) is a set of libraries and tools developed to support the development, implementation, and execution of general multimodel simulations. Using a minimal set of simulation meta-data AMSI allows for minimally intrusive work to adapt existent single-scale simulations for use in multi-scale simulations. Support for dynamic runtime operations such as single- and multi-scale adaptive properties is a key focus of AMSI. Particular focus has been spent on the development on scale-sensitive load balancing operations to allow single-scale simulations incorporated into a multi-scale simulation using AMSI to use standard load-balancing operations without affecting the integrity of the overall multi-scale simulation.

A Flexible Spatio-Temporal Model for Air Pollution with Spatial and Spatio-Temporal Covariates

OpenAIRE

Lindström, Johan; Szpiro, Adam A; Sampson, Paul D; Oron, Assaf P; Richards, Mark; Larson, Tim V; Sheppard, Lianne

2013-01-01

The development of models that provide accurate spatio-temporal predictions of ambient air pollution at small spatial scales is of great importance for the assessment of potential health effects of air pollution. Here we present a spatio-temporal framework that predicts ambient air pollution by combining data from several different monitoring networks and deterministic air pollution model(s) with geographic information system (GIS) covariates. The model presented in this paper has been implem...

Atomistic simulation of dislocation nucleation barriers from cracktips in α-Fe

International Nuclear Information System (INIS)

Gordon, Peter A; Neeraj, T; Luton, Michael J

2008-01-01

In this work, we demonstrate that activation pathways for dislocation loop nucleation from cracktips can be explored with full atomistic detail using an efficient form of the nudged elastic band method. The approach is demonstrated in detail with an example of edge emission from an Fe crack under mode II loading, wherein activation energy barriers are obtained as a function of sub-critical stress intensity and the energy barriers for loop formation are compared with 2D calculations. Activation energy barriers are also computed for an intrinsically ductile cracktip orientation under mode I loading, from which we can infer the frequency of nucleation from the cracktip

Emergence of linear elasticity from the atomistic description of matter

Energy Technology Data Exchange (ETDEWEB)

Cakir, Abdullah, E-mail: acakir@ntu.edu.sg [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore); Pica Ciamarra, Massimo [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore); Dipartimento di Scienze Fisiche, CNR–SPIN, Università di Napoli Federico II, I-80126 Napoli (Italy)

2016-08-07

We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of the fluctuations of the local elastic constants close to the jamming transition.

Emergence of linear elasticity from the atomistic description of matter

International Nuclear Information System (INIS)

Cakir, Abdullah; Pica Ciamarra, Massimo

2016-01-01

We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of the fluctuations of the local elastic constants close to the jamming transition.

Spatiotemporal dynamics of large-scale brain activity

Science.gov (United States)

Neuman, Jeremy

Understanding the dynamics of large-scale brain activity is a tough challenge. One reason for this is the presence of an incredible amount of complexity arising from having roughly 100 billion neurons connected via 100 trillion synapses. Because of the extremely high number of degrees of freedom in the nervous system, the question of how the brain manages to properly function and remain stable, yet also be adaptable, must be posed. Neuroscientists have identified many ways the nervous system makes this possible, of which synaptic plasticity is possibly the most notable one. On the other hand, it is vital to understand how the nervous system also loses stability, resulting in neuropathological diseases such as epilepsy, a disease which affects 1% of the population. In the following work, we seek to answer some of these questions from two different perspectives. The first uses mean-field theory applied to neuronal populations, where the variables of interest are the percentages of active excitatory and inhibitory neurons in a network, to consider how the nervous system responds to external stimuli, self-organizes and generates epileptiform activity. The second method uses statistical field theory, in the framework of single neurons on a lattice, to study the concept of criticality, an idea borrowed from physics which posits that in some regime the brain operates in a collectively stable or marginally stable manner. This will be examined in two different neuronal networks with self-organized criticality serving as the overarching theme for the union of both perspectives. One of the biggest problems in neuroscience is the question of to what extent certain details are significant to the functioning of the brain. These details give rise to various spatiotemporal properties that at the smallest of scales explain the interaction of single neurons and synapses and at the largest of scales describe, for example, behaviors and sensations. In what follows, we will shed some

Second-order analysis of structured inhomogeneous spatio-temporal point processes

DEFF Research Database (Denmark)

Møller, Jesper; Ghorbani, Mohammad

Statistical methodology for spatio-temporal point processes is in its infancy. We consider second-order analysis based on pair correlation functions and K-functions for first general inhomogeneous spatio-temporal point processes and second inhomogeneous spatio-temporal Cox processes. Assuming...... spatio-temporal separability of the intensity function, we clarify different meanings of second-order spatio-temporal separability. One is second-order spatio-temporal independence and relates e.g. to log-Gaussian Cox processes with an additive covariance structure of the underlying spatio......-temporal Gaussian process. Another concerns shot-noise Cox processes with a separable spatio-temporal covariance density. We propose diagnostic procedures for checking hypotheses of second-order spatio-temporal separability, which we apply on simulated and real data (the UK 2001 epidemic foot and mouth disease data)....

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

Energy Technology Data Exchange (ETDEWEB)

Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludig–Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

2015-11-14

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved—up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.

Parametric spatiotemporal oscillation in reaction-diffusion systems.

Science.gov (United States)

Ghosh, Shyamolina; Ray, Deb Shankar

2016-03-01

We consider a reaction-diffusion system in a homogeneous stable steady state. On perturbation by a time-dependent sinusoidal forcing of a suitable scaling parameter the system exhibits parametric spatiotemporal instability beyond a critical threshold frequency. We have formulated a general scheme to calculate the threshold condition for oscillation and the range of unstable spatial modes lying within a V-shaped region reminiscent of Arnold's tongue. Full numerical simulations show that depending on the specificity of nonlinearity of the models, the instability may result in time-periodic stationary patterns in the form of standing clusters or spatially localized breathing patterns with characteristic wavelengths. Our theoretical analysis of the parametric oscillation in reaction-diffusion system is corroborated by full numerical simulation of two well-known chemical dynamical models: chlorite-iodine-malonic acid and Briggs-Rauscher reactions.

Aspects of second-order analysis of structured inhomogeneous spatio-temporal processes

DEFF Research Database (Denmark)

Møller, Jesper; Ghorbani, Mohammad

2012-01-01

Statistical methodology for spatio-temporal point processes is in its infancy. We consider second-order analysis based on pair correlation functions and K-functions for general inhomogeneous spatio-temporal point processes and for inhomogeneous spatio-temporal Cox processes. Assuming spatio......-temporal separability of the intensity function, we clarify different meanings of second-order spatio-temporal separability. One is second-order spatio-temporal independence and relates to log-Gaussian Cox processes with an additive covariance structure of the underlying spatio-temporal Gaussian process. Another...... concerns shot-noise Cox processes with a separable spatio-temporal covariance density. We propose diagnostic procedures for checking hypotheses of second-order spatio-temporal separability, which we apply on simulated and real data....

Atomistic characterization of pseudoelasticity and shape memory in NiTi nanopillars

International Nuclear Information System (INIS)

Zhong Yuan; Gall, Ken; Zhu Ting

2012-01-01

Molecular dynamics simulations are performed to study the atomistic mechanisms governing the pseudoelasticity and shape memory in nickel–titanium (NiTi) nanostructures. For a 〈1 1 0〉 – oriented nanopillar subjected to compressive loading–unloading, we observe either a pseudoelastic or shape memory response, depending on the applied strain and temperature that control the reversibility of phase transformation and deformation twinning. We show that irreversible twinning arises owing to the dislocation pinning of twin boundaries, while hierarchically twinned microstructures facilitate the reversible twinning. The nanoscale size effects are manifested as the load serration, stress plateau and large hysteresis loop in stress–strain curves that result from the high stresses required to drive the nucleation-controlled phase transformation and deformation twinning in nanosized volumes. Our results underscore the importance of atomistically resolved modeling for understanding the phase and deformation reversibilities that dictate the pseudoelasticity and shape memory behavior in nanostructured shape memory alloys.

The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

International Nuclear Information System (INIS)

Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian; Sugii, Taisuke

2015-01-01

We investigate the volumetric glass transition temperature T g in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T g increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T g in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T g is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment

Lattice Thermal Conductivity of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2 from Atomistic Simulations

Science.gov (United States)

Lawson, John W.; Daw, Murray S.; Bauschlicher, Charles W.

2012-01-01

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

Spatiotemporal multiscaling analysis of impurity transport in plasma turbulence using proper orthogonal decomposition

International Nuclear Information System (INIS)

Futatani, S.; Benkadda, S.; Del-Castillo-Negrete, D.

2009-01-01

The spatiotemporal multiscale dynamics of the turbulent transport of impurities is studied in the context of the collisional drift wave turbulence. Two turbulence regimes are considered: a quasihydrodynamic regime and a quasiadiabatic regime. The impurity is assumed to be a passive scalar advected by the corresponding ExB turbulent flow in the presence of diffusion. Two mixing scenarios are studied: a freely decaying case, and a forced case in which the scalar is forced by an externally imposed gradient. The results of the direct numerical simulations are analyzed using proper orthogonal decomposition (POD) techniques. The multiscale analysis is based on a space-time separable POD of the impurity field. The low rank spatial POD eigenfunctions capture the large scale coherent structures and the high rank eigenfunctions capture the small scale fluctuations. The temporal evolution at each scale is dictated by the corresponding temporal POD eigenfunctions. Contrary to the decaying case in which the POD spectrum decays fast, the spectrum in the forced case is relatively flat. The most striking difference between these two mixing scenarios is in the temporal dynamics of the small scale structures. In the decaying case the POD reveals the presence of 'bursty' dynamics in which successively small (high POD rank) scales are intermittently activated during the mixing process. On the other hand, in the forced simulations the temporal dynamics exhibits stationary fluctuations. Spatial intermittency or 'patchiness' in the mixing process characterizes the distribution of the passive tracer in the decaying quasihydrodynamic regime. In particular, in this case the probability distribution function of the low rank POD spatial reconstruction error is non-Gaussian. The spatiotemporal POD scales exhibit a diffusive-type scaling in the quasiadiabatic regime. However, this scaling seems to be absent in the quasihydrodynamic regime that shows no scaling (in the decaying case) or two

Impact of Sub-grid Soil Textural Properties on Simulations of Hydrological Fluxes at the Continental Scale Mississippi River Basin

Science.gov (United States)

Kumar, R.; Samaniego, L. E.; Livneh, B.

2013-12-01

Knowledge of soil hydraulic properties such as porosity and saturated hydraulic conductivity is required to accurately model the dynamics of near-surface hydrological processes (e.g. evapotranspiration and root-zone soil moisture dynamics) and provide reliable estimates of regional water and energy budgets. Soil hydraulic properties are commonly derived from pedo-transfer functions using soil textural information recorded during surveys, such as the fractions of sand and clay, bulk density, and organic matter content. Typically large scale land-surface models are parameterized using a relatively coarse soil map with little or no information on parametric sub-grid variability. In this study we analyze the impact of sub-grid soil variability on simulated hydrological fluxes over the Mississippi River Basin (≈3,240,000 km2) at multiple spatio-temporal resolutions. A set of numerical experiments were conducted with the distributed mesoscale hydrologic model (mHM) using two soil datasets: (a) the Digital General Soil Map of the United States or STATSGO2 (1:250 000) and (b) the recently collated Harmonized World Soil Database based on the FAO-UNESCO Soil Map of the World (1:5 000 000). mHM was parameterized with the multi-scale regionalization technique that derives distributed soil hydraulic properties via pedo-transfer functions and regional coefficients. Within the experimental framework, the 3-hourly model simulations were conducted at four spatial resolutions ranging from 0.125° to 1°, using meteorological datasets from the NLDAS-2 project for the time period 1980-2012. Preliminary results indicate that the model was able to capture observed streamflow behavior reasonably well with both soil datasets, in the major sub-basins (i.e. the Missouri, the Upper Mississippi, the Ohio, the Red, and the Arkansas). However, the spatio-temporal patterns of simulated water fluxes and states (e.g. soil moisture, evapotranspiration) from both simulations, showed marked

Evaluation of white spot syndrome virus variable DNA loci as molecular markers of virus spread at intermediate spatiotemporal scales

NARCIS (Netherlands)

Bui Thi Minh Dieu,; Marks, H.; Zwart, M.P.; Vlak, J.M.

2010-01-01

Variable genomic loci have been employed in a number of molecular epidemiology studies of white spot syndrome virus (WSSV), but it is unknown which loci are suitable molecular markers for determining WSSV spread on different spatiotemporal scales. Although previous work suggests that multiple

Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China.

Science.gov (United States)

Cao, Chunxiang; Chen, Wei; Zheng, Sheng; Zhao, Jian; Wang, Jinfeng; Cao, Wuchun

2016-01-01

Severe acute respiratory syndrome (SARS) is one of the most severe emerging infectious diseases of the 21st century so far. SARS caused a pandemic that spread throughout mainland China for 7 months, infecting 5318 persons in 194 administrative regions. Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME) method. The BME reveals that SARS outbreaks show autocorrelation within certain spatial and temporal distances. We use BME to fit a theoretical covariance model that has a sine hole spatial component and exponential temporal component and obtain the weights of geographical and temporal autocorrelation factors. Using the covariance model, SARS dynamics were estimated and simulated under the most probable conditions. Our study suggests that SARS transmission varies in its epidemiological characteristics and SARS outbreak distributions exhibit palpable clusters on both spatial and temporal scales. In addition, the BME modelling demonstrates that SARS transmission features are affected by spatial heterogeneity, so we analyze potential causes. This may benefit epidemiological control of pandemic infectious diseases.

Multistage reaction pathways in detonating high explosives

International Nuclear Information System (INIS)

Li, Ying; Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya

2014-01-01

Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N 2 and H 2 O within ∼10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct unimolecular and intermolecular reaction pathways, respectively, for the rapid N 2 and H 2 O productions

Multistage reaction pathways in detonating high explosives

Energy Technology Data Exchange (ETDEWEB)

Li, Ying [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States)

2014-11-17

Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N{sub 2} and H{sub 2}O within ∼10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct unimolecular and intermolecular reaction pathways, respectively, for the rapid N{sub 2} and H{sub 2}O productions.

On the use of atomistic simulations to aid bulk metallic glasses structural elucidation with solid-state NMR.

Science.gov (United States)

Ferreira, Ary R; Rino, José P

2017-08-24

Solid-state nuclear magnetic resonance (ssNMR) experimental 27 Al metallic shifts reported in the literature for bulk metallic glasses (BMGs) were revisited in the light of state-of-the-art atomistic simulations. In a consistent way, the Gauge-Including Projector Augmented-Wave (GIPAW) method was applied in conjunction with classical molecular dynamics (CMD). A series of Zr-Cu-Al alloys with low Al concentrations were selected as case study systems, for which realistic CMD derived structural models were used for a short- and medium-range order mining. That initial procedure allowed the detection of trends describing changes on the microstructure of the material upon Al alloying, which in turn were used to guide GIPAW calculations with a set of abstract systems in the context of ssNMR. With essential precision and accuracy, the ab initio simulations also yielded valuable trends from the electronic structure point of view, which enabled an overview of the bonding nature of Al-centered clusters as well as its influence on the experimental ssNMR outcomes. The approach described in this work might promote the use of ssNMR spectroscopy in research on glassy metals. Moreover, the results presented demonstrate the possibility to expand the applications of this technique, with deeper insight into nuclear interactions and less speculative assignments.

On the atomistic mechanisms of alkane (methane-pentane) separation by distillation: a molecular dynamics study.

Science.gov (United States)

Zahn, Dirk

2007-11-01

Insights into the liquid-vapor transformation of methane-pentane mixtures were obtained from transition path sampling molecular dynamics simulations. This case study of the boiling of non-azeotropic mixtures demonstrates an unprejudiced identification of the atomistic mechanisms of phase separation in the course of vaporization which form the basis of distillation processes. From our simulations we observe spontaneous segregation events in the liquid mixture to trigger vapor nucleation. The formation of vapor domains stabilizes and further promotes the separation process by preferential evaporation of methane molecules. While this discrimination holds for all mixtures of different composition studied, a full account of the boiling process requires a more complex picture. At low methane concentration the nucleation of the vapor domains includes both methane and pentane molecules. The pentane molecules, however, tend to form small aggregates and undergo rapid re-condensation within picoseconds to nanoseconds scales. Accordingly, two aspects of selectivity accounting for methane-pentane separation in the course of liquid-vapor transformations were made accessible to molecular dynamics simulations: spontaneous segregation in the liquid phase leading to selective vapor nucleation and growth favoring methane vaporization and selective re-condensation of pentane molecules.

Clinimetric properties of the Tinetti Mobility Test, Four Square Step Test, Activities-specific Balance Confidence Scale, and spatiotemporal gait measures in individuals with Huntington's disease.

Science.gov (United States)

Kloos, Anne D; Fritz, Nora E; Kostyk, Sandra K; Young, Gregory S; Kegelmeyer, Deb A

2014-09-01

Individuals with Huntington's disease (HD) experience balance and gait problems that lead to falls. Clinicians currently have very little information about the reliability and validity of outcome measures to determine the efficacy of interventions that aim to reduce balance and gait impairments in HD. This study examined the reliability and concurrent validity of spatiotemporal gait measures, the Tinetti Mobility Test (TMT), Four Square Step Test (FSST), and Activities-specific Balance Confidence (ABC) Scale in individuals with HD. Participants with HD [n = 20; mean age ± SD=50.9 ± 13.7; 7 male] were tested on spatiotemporal gait measures and the TMT, FSST, and ABC Scale before and after a six week period to determine test-retest reliability and minimal detectable change (MDC) values. Linear relationships between gait and clinical measures were estimated using Pearson's correlation coefficients. Spatiotemporal gait measures, the TMT total and the FSST showed good to excellent test-retest reliability (ICC > 0.75). MDC values were 0.30 m/s and 0.17 m/s for velocity in forward and backward walking respectively, four points for the TMT, and 3s for the FSST. The TMT and FSST were highly correlated with most spatiotemporal measures. The ABC Scale demonstrated lower reliability and less concurrent validity than other measures. The high test-retest reliability over a six week period and concurrent validity between the TMT, FSST, and spatiotemporal gait measures suggest that the TMT and FSST may be useful outcome measures for future intervention studies in ambulatory individuals with HD. Copyright © 2014 Elsevier B.V. All rights reserved.

Deductive multiscale simulation using order parameters

Science.gov (United States)

Ortoleva, Peter J.

2017-05-16

Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

Large scale stochastic spatio-temporal modelling with PCRaster

NARCIS (Netherlands)

Karssenberg, D.J.; Drost, N.; Schmitz, O.; Jong, K. de; Bierkens, M.F.P.

2013-01-01

PCRaster is a software framework for building spatio-temporal models of land surface processes (http://www.pcraster.eu). Building blocks of models are spatial operations on raster maps, including a large suite of operations for water and sediment routing. These operations are available to model

Probing the Mechanism of pH-Induced Large-Scale Conformational Changes in Dengue Virus Envelope Protein Using Atomistic Simulations

Science.gov (United States)

Prakash, Meher K.; Barducci, Alessandro; Parrinello, Michele

2010-01-01

Abstract One of the key steps in the infection of the cell by dengue virus is a pH-induced conformational change of the viral envelope proteins. These envelope proteins undergo a rearrangement from a dimer to a trimer, with large conformational changes in the monomeric unit. In this article, metadynamics simulations were used to enable us to understand the mechanism of these large-scale changes in the monomer. By using all-atom, explicit solvent simulations of the monomers, the stability of the protein structure is studied under low and high pH conditions. Free energy profiles obtained along appropriate collective coordinates demonstrate that pH affects the domain interface in both the conformations of E monomer, stabilizing one and destabilizing the other. These simulations suggest a mechanism with an intermediate detached state between the two monomeric structures. Using further analysis, we comment on the key residue interactions responsible for the instability and the pH-sensing role of a histidine that could not otherwise be studied experimentally. The insights gained from this study and methodology can be extended for studying similar mechanisms in the E proteins of the other members of class II flavivirus family. PMID:20643078

Atomistic simulations of thermal transport in Si and SiGe based materials: From bulk to nanostructures

Science.gov (United States)

Savic, Ivana; Mingo, Natalio; Donadio, Davide; Galli, Giulia

2010-03-01

It has been recently proposed that Si and SiGe based nanostructured materials may exhibit low thermal conductivity and overall promising properties for thermoelectric applications. Hence there is a considerable interest in developing accurate theoretical and computational methods which can help interpret recent measurements, identify the physical origin of the reduced thermal conductivity, as well as shed light on the interplay between disorder and nanostructuring in determining a high figure of merit. In this work, we investigate the capability of an atomistic Green's function method [1] to describe phonon transport in several types of Si and SiGe based systems: amorphous Si, SiGe alloys, planar and nanodot Si/SiGe multilayers. We compare our results with experimental data [2,3], and with the findings of molecular dynamics simulations and calculations based on the Boltzmann transport equation. [1] I. Savic, N. Mingo, and D. A. Stewart, Phys. Rev. Lett. 101, 165502 (2008). [2] S.-M. Lee, D. G. Cahill, and R. Venkatasubramanian, Appl. Phys. Lett. 70, 2957 (1997). [3] G. Pernot et al., submitted.

Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal

International Nuclear Information System (INIS)

Huang, Liangliang; Gubbins, Keith E.; Seredych, Mykola; Bandosz, Teresa J.; Duin, Adri C. T. van; Lu, Xiaohua

2013-01-01

The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H 2 S and H 2 O/H 2 S mixtures on GO materials and compare the results with experiment. We find that H 2 S molecules dissociate on the carbonyl functional groups, and H 2 O, CO 2 , and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H 2 O/H 2 S mixtures, H 2 O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H 2 S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials

Automated Algorithms for Quantum-Level Accuracy in Atomistic Simulations: LDRD Final Report.

Energy Technology Data Exchange (ETDEWEB)

Thompson, Aidan Patrick; Schultz, Peter Andrew; Crozier, Paul; Moore, Stan Gerald; Swiler, Laura Painton; Stephens, John Adam; Trott, Christian Robert; Foiles, Stephen Martin; Tucker, Garritt J. (Drexel University)

2014-09-01

This report summarizes the result of LDRD project 12-0395, titled "Automated Algorithms for Quantum-level Accuracy in Atomistic Simulations." During the course of this LDRD, we have developed an interatomic potential for solids and liquids called Spectral Neighbor Analysis Poten- tial (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The SNAP coef- ficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. Global optimization methods in the DAKOTA software package are used to seek out good choices of hyperparameters that define the overall structure of the SNAP potential. FitSnap.py, a Python-based software pack- age interfacing to both LAMMPS and DAKOTA is used to formulate the linear regression problem, solve it, and analyze the accuracy of the resultant SNAP potential. We describe a SNAP potential for tantalum that accurately reproduces a variety of solid and liquid properties. Most significantly, in contrast to existing tantalum potentials, SNAP correctly predicts the Peierls barrier for screw dislocation motion. We also present results from SNAP potentials generated for indium phosphide (InP) and silica (SiO 2 ). We describe efficient algorithms for calculating SNAP forces and energies in molecular dynamics simulations using massively parallel computers

Extending atomistic scale chemistry to mesoscale model of condensed-phase deflagration

Science.gov (United States)

Joshi, Kaushik; Chaudhuri, Santanu

2017-01-01

Predictive simulations connecting chemistry that follow the shock or thermal initiation of energetic materials to subsequent deflagration or detonation events is currently outside the realm of possibilities. Molecular dynamics and first-principles based dynamics have made progress in understanding reactions in picosecond to nanosecond time scale. Results from thermal ignition of different phases of RDX show a complex reaction network and emergence of a deterministic behavior for critical temperature before ignition and hot spot growth rates. The kinetics observed is dependent on the hot spot temperature, system size and thermal conductivity. For cases where ignition is observed, the incubation period is dominated by intermolecular and intramolecular hydrogen transfer reactions. The gradual temperature and pressure increase in the incubation period is accompanied by accumulation of heavier polyradicals. The challenge of connecting such chemistry in mesoscale simulations remain in reducing the complexity of chemistry. The hot spot growth kinetics in RDX grains and interfaces is an important challenge for reactive simulations aiming to fill in the gaps in our knowledge in the nanoseconds to microseconds time scale. The results discussed indicate that the mesoscale chemistry may include large polyradical molecules in dense reactive mix reaching an instability point at certain temperatures and pressures.

Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin–myosin light chain interaction

International Nuclear Information System (INIS)

Delmotte, A; Barahona, M; Tate, E W; Yaliraki, S N

2011-01-01

Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the intricate coupling between the different scales. Starting from a physico-chemical atomistic network of interactions that encodes the structure of the protein, we introduce a methodology based on multi-scale graph partitioning that can uncover partitions and levels of organization of proteins that span the whole range of scales, revealing biological features occurring at different levels of organization and tracking their effect across scales. Additionally, we introduce a measure of robustness to quantify the relevance of the partitions through the generation of biochemically-motivated surrogate random graph models. We apply the method to four distinct conformations of myosin tail interacting protein, a protein from the molecular motor of the malaria parasite, and study properties that have been experimentally addressed such as the closing mechanism, the presence of conserved clusters, and the identification through computational mutational analysis of key residues for binding

Controlling spatiotemporal chaos in one- and two-dimensional coupled logistic map lattices

International Nuclear Information System (INIS)

Astakhov, V.V.; Anishchenko, V.S.; Strelkova, G.I.; Shabunin, A.V.

1996-01-01

A method of control of spatiotemporal chaos in lattices of coupled maps is proposed in this work. Forms of spatiotemporal perturbations of a system parameter are analytically determined for one- and two-dimensional logistic map lattices with different kinds of coupling to stabilize chosen spatiotemporal states previously unstable. The results are illustrated by numerical simulation. Controlled transition from the regime of spatiotemporal chaos to the previously chosen regular spatiotemporal patterns is demonstrated. copyright 1996 American Institute of Physics

Spatio-temporal variability of soil water content on the local scale in a Mediterranean mountain area (Vallcebre, North Eastern Spain). How different spatio-temporal scales reflect mean soil water content

Science.gov (United States)

Molina, Antonio J.; Latron, Jérôme; Rubio, Carles M.; Gallart, Francesc; Llorens, Pilar

2014-08-01

As a result of complex human-land interactions and topographic variability, many Mediterranean mountain catchments are covered by agricultural terraces that have locally modified the soil water content dynamic. Understanding these local-scale dynamics helps us grasp better how hydrology behaves on the catchment scale. Thus, this study examined soil water content variability in the upper 30 cm of the soil on a Mediterranean abandoned terrace in north-east Spain. Using a dataset of high spatial (regular grid of 128 automatic TDR probes at 2.5 m intervals) and temporal (20-min time step) resolution, gathered throughout a 84-day period, the spatio-temporal variability of soil water content at the local scale and the way that different spatio-temporal scales reflect the mean soil water content were investigated. Soil water content spatial variability and its relation to wetness conditions were examined, along with the spatial structuring of the soil water content within the terrace. Then, the ability of single probes and of different combinations of spatial measurements (transects and grids) to provide a good estimate of mean soil water content on the terrace scale was explored by means of temporal stability analyses. Finally, the effect of monitoring frequency on the magnitude of detectable daily soil water content variations was studied. Results showed that soil water content spatial variability followed a bimodal pattern of increasing absolute variability with increasing soil water content. In addition, a linear trend of decreasing soil water content as the distance from the inner part of the terrace increased was identified. Once this trend was subtracted, resulting semi-variograms suggested that the spatial resolution examined was too high to appreciate spatial structuring in the data. Thus, the spatial pattern should be considered as random. Of all the spatial designs tested, the 10 × 10 m mesh grid (9 probes) was considered the most suitable option for a good

Atomistic Origin of Rate-Dependent Serrated Plastic Flow in Metallic Glasses

Directory of Open Access Journals (Sweden)

Yao YG

2008-01-01

Full Text Available Abstract Nanoindentation simulations on a binary metallic glass were performed under various strain rates by using molecular dynamics. The rate-dependent serrated plastic flow was clearly observed, and the spatiotemporal behavior of its underlying irreversible atomic rearrangement was probed. Our findings clearly validate that the serration is a temporally inhomogeneous characteristic of such rearrangements and not directly dependent on the resultant shear-banding spatiality. The unique spatiotemporal distribution of shear banding during nanoindentation is highlighted in terms of the potential energy landscape (PEL theory.

A Multi-Stage Method for Connecting Participatory Sensing and Noise Simulations

Directory of Open Access Journals (Sweden)

Mingyuan Hu

2015-01-01

Full Text Available Most simulation-based noise maps are important for official noise assessment but lack local noise characteristics. The main reasons for this lack of information are that official noise simulations only provide information about expected noise levels, which is limited by the use of large-scale monitoring of noise sources, and are updated infrequently. With the emergence of smart cities and ubiquitous sensing, the possible improvements enabled by sensing technologies provide the possibility to resolve this problem. This study proposed an integrated methodology to propel participatory sensing from its current random and distributed sampling origins to professional noise simulation. The aims of this study were to effectively organize the participatory noise data, to dynamically refine the granularity of the noise features on road segments (e.g., different portions of a road segment, and then to provide a reasonable spatio-temporal data foundation to support noise simulations, which can be of help to researchers in understanding how participatory sensing can play a role in smart cities. This study first discusses the potential limitations of the current participatory sensing and simulation-based official noise maps. Next, we explain how participatory noise data can contribute to a simulation-based noise map by providing (1 spatial matching of the participatory noise data to the virtual partitions at a more microscopic level of road networks; (2 multi-temporal scale noise estimations at the spatial level of virtual partitions; and (3 dynamic aggregation of virtual partitions by comparing the noise values at the relevant temporal scale to form a dynamic segmentation of each road segment to support multiple spatio-temporal noise simulations. In this case study, we demonstrate how this method could play a significant role in a simulation-based noise map. Together, these results demonstrate the potential benefits of participatory noise data as dynamic

Multiscale Modeling of Carbon/Phenolic Composite Thermal Protection Materials: Atomistic to Effective Properties

Science.gov (United States)

Arnold, Steven M.; Murthy, Pappu L.; Bednarcyk, Brett A.; Lawson, John W.; Monk, Joshua D.; Bauschlicher, Charles W., Jr.

2016-01-01

Next generation ablative thermal protection systems are expected to consist of 3D woven composite architectures. It is well known that composites can be tailored to achieve desired mechanical and thermal properties in various directions and thus can be made fit-for-purpose if the proper combination of constituent materials and microstructures can be realized. In the present work, the first, multiscale, atomistically-informed, computational analysis of mechanical and thermal properties of a present day - Carbon/Phenolic composite Thermal Protection System (TPS) material is conducted. Model results are compared to measured in-plane and out-of-plane mechanical and thermal properties to validate the computational approach. Results indicate that given sufficient microstructural fidelity, along with lowerscale, constituent properties derived from molecular dynamics simulations, accurate composite level (effective) thermo-elastic properties can be obtained. This suggests that next generation TPS properties can be accurately estimated via atomistically informed multiscale analysis.

Atomistic modeling and simulation of the role of Be and Bi in Al diffusion in U-Mo fuel

Science.gov (United States)

Hofman, G. L.; Bozzolo, G.; Mosca, H. O.; Yacout, A. M.

2011-07-01

Within the RERTR program, previous experimental and modeling studies identified Si as the alloying addition to the Al cladding responsible for inhibiting Al interdiffusion in the UMo fuel. However, difficulties with reprocessing have rendered this choice inappropriate, leading to the need to study alternative elements. In this work, we discuss the results of an atomistic modeling effort which allows for the systematic study of several possible alloying additions. Based on the behavior observed in the phase diagrams, beryllium or bismuth additions suggest themselves as possible options to replace Si. The results of temperature-dependent simulations using the Bozzolo-Ferrante-Smith (BFS) method for the energetics for varying concentrations of either element are shown, indicating that Be could have a substantial effect in stopping Al interdiffusion, while Bi does not. Details of the calculations and the dependence of the role of each alloying addition as a function of temperature and concentration (of beryllium or bismuth in Al) are shown.

Atomistic modeling and simulation of the role of Be and Bi in Al diffusion in U-Mo fuel

Energy Technology Data Exchange (ETDEWEB)

Hofman, G.L. [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States); Bozzolo, G., E-mail: guille_bozzolo@yahoo.com [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States); Mosca, H.O. [Gerencia de Investigaciones y Aplicaciones, CNEA, Av. Gral Paz 1499, B165KNA, San Martin, Buenos Aires (Argentina); Yacout, A.M. [Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439 (United States)

2011-07-15

Within the RERTR program, previous experimental and modeling studies identified Si as the alloying addition to the Al cladding responsible for inhibiting Al interdiffusion in the UMo fuel. However, difficulties with reprocessing have rendered this choice inappropriate, leading to the need to study alternative elements. In this work, we discuss the results of an atomistic modeling effort which allows for the systematic study of several possible alloying additions. Based on the behavior observed in the phase diagrams, beryllium or bismuth additions suggest themselves as possible options to replace Si. The results of temperature-dependent simulations using the Bozzolo-Ferrante-Smith (BFS) method for the energetics for varying concentrations of either element are shown, indicating that Be could have a substantial effect in stopping Al interdiffusion, while Bi does not. Details of the calculations and the dependence of the role of each alloying addition as a function of temperature and concentration (of beryllium or bismuth in Al) are shown.

An atomistic study of the deformation behavior of tungsten nanowires

Energy Technology Data Exchange (ETDEWEB)

Xu, Shuozhi [University of California, California NanoSystems Institute, Santa Barbara, CA (United States); Su, Yanqing [University of California, Department of Mechanical Engineering, Santa Barbara, CA (United States); Chen, Dengke [Georgia Institute of Technology, GWW School of Mechanical Engineering, Atlanta, GA (United States); Li, Longlei [Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA (United States)

2017-12-15

Large-scale atomistic simulations are performed to study tensile and compressive left angle 112 right angle loading of single-crystalline nanowires in body-centered cubic tungsten (W). Effects of loading mode, wire cross-sectional shape, wire size, strain rate, and crystallographic orientations of the lateral surfaces are explored. Uniaxial deformation of a W bulk single crystal is also investigated for reference. Our results reveal a strong tension-compression asymmetry in both the stress-strain response and the deformation behavior due to different yielding/failure modes: while the nanowires fail by brittle fracture under tensile loading, they yield by nucleation of dislocations from the wire surface under compressive loading. It is found that (1) nanowires have a higher strength than the bulk single crystal; (2) with a cross-sectional size larger than 10 nm, there exists a weak dependence of strength on wire size; (3) when the wire size is equal to or smaller than 10 nm, nanowires buckle under compressive loading; (4) the cross-sectional shape, strain rate, and crystallographic orientations of the lateral surfaces affect the strength and the site of defect initiation but not the overall deformation behavior. (orig.)

General atomistic approach for modeling metal-semiconductor interfaces using density functional theory and nonequilibrium Green's function

DEFF Research Database (Denmark)

Stradi, Daniele; Martinez, Umberto; Blom, Anders

2016-01-01

Metal-semiconductor contacts are a pillar of modern semiconductor technology. Historically, their microscopic understanding has been hampered by the inability of traditional analytical and numerical methods to fully capture the complex physics governing their operating principles. Here we introduce...... an atomistic approach based on density functional theory and nonequilibrium Green's function, which includes all the relevant ingredients required to model realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via I-Vbias curve simulations. We apply...... interfaces as it neglects electron tunneling, and that finite-size atomistic models have problems in describing these interfaces in the presence of doping due to a poor representation of space-charge effects. Conversely, the present method deals effectively with both issues, thus representing a valid...

The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

Energy Technology Data Exchange (ETDEWEB)

Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt (Germany); Sugii, Taisuke, E-mail: taisuke.sugii.zs@hitachi.com [Center for Technology Innovation – Mechanical Engineering, Research & Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034 (Japan)

2015-12-28

We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.

An Atomistic Carbide-Derived Carbon Model Generated Using ReaxFF-Based Quenched Molecular Dynamics

Directory of Open Access Journals (Sweden)

Matthew W. Thompson

2017-10-01

Full Text Available We report a novel atomistic model of carbide-derived carbons (CDCs, which are nanoporous carbons with high specific surface areas, synthesis-dependent degrees of graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, and catalytic supports. These materials are heterogenous, non-ideal structures and include several important parameters that govern their performance. Therefore, a realistic model of the CDC structure is needed in order to study these systems and their nanoscale and macroscale properties with molecular simulation. We report the use of the ReaxFF reactive force field in a quenched molecular dynamics routine to generate atomistic CDC models. The pair distribution function, pore size distribution, and adsorptive properties of this model are reported and corroborated with experimental data. Simulations demonstrate that compressing the system after quenching changes the pore size distribution to better match the experimental target. Ring size distributions of this model demonstrate the prevalence of non-hexagonal carbon rings in CDCs. These effects may contrast the properties of CDCs against those of activated carbons with similar pore size distributions and explain higher energy densities of CDC-based supercapacitors.

Deformation behaviors of three-dimensional graphene honeycombs under out-of-plane compression: Atomistic simulations and predictive modeling

Science.gov (United States)

Meng, Fanchao; Chen, Cheng; Hu, Dianyin; Song, Jun

2017-12-01

Combining atomistic simulations and continuum modeling, a comprehensive study of the out-of-plane compressive deformation behaviors of equilateral three-dimensional (3D) graphene honeycombs was performed. It was demonstrated that under out-of-plane compression, the honeycomb exhibits two critical deformation events, i.e., elastic mechanical instability (including elastic buckling and structural transformation) and inelastic structural collapse. The above events were shown to be strongly dependent on the honeycomb cell size and affected by the local atomic bonding at the cell junction. By treating the 3D graphene honeycomb as a continuum cellular solid, and accounting for the structural heterogeneity and constraint at the junction, a set of analytical models were developed to accurately predict the threshold stresses corresponding to the onset of those deformation events. The present study elucidates key structure-property relationships of 3D graphene honeycombs under out-of-plane compression, and provides a comprehensive theoretical framework to predictively analyze their deformation responses, and more generally, offers critical new knowledge for the rational bottom-up design of 3D networks of two-dimensional nanomaterials.

Thermally activated magnetization reversal in monatomic magnetic chains on surfaces studied by classical atomistic spin-dynamics simulations

International Nuclear Information System (INIS)

Bauer, David S G; Mavropoulos, Phivos; Bluegel, Stefan; Lounis, Samir

2011-01-01

We analyse the spontaneous magnetization reversal of supported monatomic chains of finite length due to thermal fluctuations via atomistic spin-dynamics simulations. Our approach is based on the integration of the Landau-Lifshitz equation of motion of a classical spin Hamiltonian in the presence of stochastic forces. The associated magnetization lifetime is found to obey an Arrhenius law with an activation barrier equal to the domain wall energy in the chain. For chains longer than one domain wall width, the reversal is initiated by nucleation of a reversed magnetization domain primarily at the chain edge followed by a subsequent propagation of the domain wall to the other edge in a random-walk fashion. This results in a linear dependence of the lifetime on the chain length, if the magnetization correlation length is not exceeded. We studied chains of uniaxial and triaxial anisotropy and found that a triaxial anisotropy leads to a reduction of the magnetization lifetime due to a higher reversal attempt rate, even though the activation barrier is not changed.

Achievement report for fiscal 1998 on research and development project for university coordinated type industrial science technologies. Research and development on platform for designing high functional materials (development for practical use of technologies related to rationalization of energy use); 1998 nendo kokino zairyo sekkei platform no kenkyu kaihatsu. Energy shiyo gorikia kankei gijutsu jitsuyoka kaihatsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-03-01

This paper reports research achievements in fiscal 1998 for a platform for designing high functional materials. Since coarse-grained models used in molecular dynamics (MD) simulation are diversified depending on materials, phenomena and properties, a general purpose MD engine that can simulate them freely was designed. Methods were developed to determine the potentials of coarse-grained models from the atomistic models. In polymer melts, very slow movements caused by entanglements have a substantially important role, which are difficult to be studied by usual MD simulations. Therefore, fiscal 1998 has devised a coarse-grained model to handle slow movements of straight-chain polymers, and a rheological forecast program was prepared. Studies are also being made on meso-scale structures sufficiently large as compared to atoms and on dynamic property forecast. Works were carried out to develop a simulator, in which polymeric phenomena with large spatio-temporal scale are applied with a continuity model to solve the equation thereof. Improvements were given on the hardware/software environments required for developing simulation engines and platforms for mesoscopic region. (NEDO)

Analysis of Spatiotemporal Characteristics of Pandemic SARS Spread in Mainland China

Directory of Open Access Journals (Sweden)

Chunxiang Cao

2016-01-01

Full Text Available Severe acute respiratory syndrome (SARS is one of the most severe emerging infectious diseases of the 21st century so far. SARS caused a pandemic that spread throughout mainland China for 7 months, infecting 5318 persons in 194 administrative regions. Using detailed mainland China epidemiological data, we study spatiotemporal aspects of this person-to-person contagious disease and simulate its spatiotemporal transmission dynamics via the Bayesian Maximum Entropy (BME method. The BME reveals that SARS outbreaks show autocorrelation within certain spatial and temporal distances. We use BME to fit a theoretical covariance model that has a sine hole spatial component and exponential temporal component and obtain the weights of geographical and temporal autocorrelation factors. Using the covariance model, SARS dynamics were estimated and simulated under the most probable conditions. Our study suggests that SARS transmission varies in its epidemiological characteristics and SARS outbreak distributions exhibit palpable clusters on both spatial and temporal scales. In addition, the BME modelling demonstrates that SARS transmission features are affected by spatial heterogeneity, so we analyze potential causes. This may benefit epidemiological control of pandemic infectious diseases.

Spatiotemporal bioeconomic performance of artificial shelters in a small-scale, rights-based managed Caribbean spiny lobster (Panulirus argus fishery

Directory of Open Access Journals (Sweden)

Maren Headley

2017-03-01

Full Text Available This study presents a bioeconomic analysis of artificial shelter performance in a fishery targeting a spiny lobster meta-population, with spatially allocated, individual exclusive benthic property rights for shelter introduction and harvest of species. Insights into fishers’ short-run decisions and fishing strategies are also provided. Spatiotemporal bioeconomic performance of shelters located in ten fishing areas during four seasons was compared using two-way ANOVAs and Pearson correlations. Results show that there was spatiotemporal heterogeneity in bioeconomic variables among fishing areas, with mean catch per unit effort (CPUE, kg shelter–1 ranging from 0.42 kg to 1.3 kg per trip, mean quasi-profits of variable costs per shelter harvested ranging from USD6.00 to USD19.57 per trip, and mean quasi-profits of variable costs ranging from USD338 to USD1069 per trip. Positive moderate correlations between shelter density and CPUE (kg shelter–1 km–2 were found. Bioeconomic performance of the shelters was influenced by spatiotemporal resource abundance and distribution, fishing area location in relation to the port, shelter density, heterogeneous fishing strategies and the management system. The results provide empirical information on the spatiotemporal performance of shelters and fishing strategies and can contribute to management at the local-scale of a meta-population distributed throughout the Caribbean Sea and Gulf of Mexico.

Irradiation-induced void evolution in iron: A phase-field approach with atomistic derived parameters

International Nuclear Information System (INIS)

Wang Yuan-Yuan; Ding Jian-Hua; Huang Shao-Song; Zhao Ji-Jun; Liu Wen-Bo; Ke Xiao-Qin; Wang Yun-Zhi; Zhang Chi

2017-01-01

A series of material parameters are derived from atomistic simulations and implemented into a phase field (PF) model to simulate void evolution in body-centered cubic (bcc) iron subjected to different irradiation doses at different temperatures. The simulation results show good agreement with experimental observations — the porosity as a function of temperature varies in a bell-shaped manner and the void density monotonically decreases with increasing temperatures; both porosity and void density increase with increasing irradiation dose at the same temperature. Analysis reveals that the evolution of void number and size is determined by the interplay among the production, diffusion and recombination of vacancy and interstitial. (paper)

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

Science.gov (United States)

Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

2016-12-01

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web , and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

Molecular Simulations of Cyclic Loading Behavior of Carbon Nanotubes Using the Atomistic Finite Element Method

Directory of Open Access Journals (Sweden)

Jianfeng Wang

2009-01-01

Full Text Available The potential applications of carbon nanotubes (CNT in many engineered bionanomaterials and electromechanical devices have imposed an urgent need on the understanding of the fatigue behavior and mechanism of CNT under cyclic loading conditions. To date, however, very little work has been done in this field. This paper presents the results of a theoretical study on the behavior of CNT subject to cyclic tensile and compressive loads using quasi-static molecular simulations. The Atomistic Finite Element Method (AFEM has been applied in the study. It is shown that CNT exhibited extreme cyclic loading resistance with yielding strain and strength becoming constant within limited number of loading cycles. Viscoelastic behavior including nonlinear elasticity, hysteresis, preconditioning (stress softening, and large strain have been observed. Chiral symmetry was found to have appreciable effects on the cyclic loading behavior of CNT. Mechanisms of the observed behavior have been revealed by close examination of the intrinsic geometric and mechanical features of tube structure. It was shown that the accumulated residual defect-free morphological deformation was the primary mechanism responsible for the cyclic failure of CNT, while the bond rotating and stretching experienced during loading/unloading played a dominant role on the strength, strain and modulus behavior of CNT.

Control algorithm for multiscale flow simulations of water

DEFF Research Database (Denmark)

Kotsalis, E. M.; Walther, Jens Honore; Kaxiras, E.

2009-01-01

We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions...

Continuum simulations of water flow past fullerene molecules

DEFF Research Database (Denmark)

Popadic, A.; Praprotnik, M.; Koumoutsakos, P.

2015-01-01

We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...... as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow...

Evaluating variability with atomistic simulations: the effect of potential and calculation methodology on the modeling of lattice and elastic constants

Science.gov (United States)

Hale, Lucas M.; Trautt, Zachary T.; Becker, Chandler A.

2018-07-01

Atomistic simulations using classical interatomic potentials are powerful investigative tools linking atomic structures to dynamic properties and behaviors. It is well known that different interatomic potentials produce different results, thus making it necessary to characterize potentials based on how they predict basic properties. Doing so makes it possible to compare existing interatomic models in order to select those best suited for specific use cases, and to identify any limitations of the models that may lead to unrealistic responses. While the methods for obtaining many of these properties are often thought of as simple calculations, there are many underlying aspects that can lead to variability in the reported property values. For instance, multiple methods may exist for computing the same property and values may be sensitive to certain simulation parameters. Here, we introduce a new high-throughput computational framework that encodes various simulation methodologies as Python calculation scripts. Three distinct methods for evaluating the lattice and elastic constants of bulk crystal structures are implemented and used to evaluate the properties across 120 interatomic potentials, 18 crystal prototypes, and all possible combinations of unique lattice site and elemental model pairings. Analysis of the results reveals which potentials and crystal prototypes are sensitive to the calculation methods and parameters, and it assists with the verification of potentials, methods, and molecular dynamics software. The results, calculation scripts, and computational infrastructure are self-contained and openly available to support researchers in performing meaningful simulations.

Optimizing Cruising Routes for Taxi Drivers Using a Spatio-Temporal Trajectory Model

Directory of Open Access Journals (Sweden)

Liang Wu

2017-11-01

Full Text Available Much of the taxi route-planning literature has focused on driver strategies for finding passengers and determining the hot spot pick-up locations using historical global positioning system (GPS trajectories of taxis based on driver experience, distance from the passenger drop-off location to the next passenger pick-up location and the waiting times at recommended locations for the next passenger. The present work, however, considers the average taxi travel speed mined from historical taxi GPS trajectory data and the allocation of cruising routes to more than one taxi driver in a small-scale region to neighboring pick-up locations. A spatio-temporal trajectory model with load balancing allocations is presented to not only explore pick-up/drop-off information but also provide taxi drivers with cruising routes to the recommended pick-up locations. In simulation experiments, our study shows that taxi drivers using cruising routes recommended by our spatio-temporal trajectory model can significantly reduce the average waiting time and travel less distance to quickly find their next passengers, and the load balancing strategy significantly alleviates road loads. These objective measures can help us better understand spatio-temporal traffic patterns and guide taxi navigation.

Nonreciprocal Thermal Material by Spatiotemporal Modulation

Science.gov (United States)

Torrent, Daniel; Poncelet, Olivier; Batsale, Jean-Chirstophe

2018-03-01

The thermal properties of a material with a spatiotemporal modulation, in the form of a traveling wave, in both the thermal conductivity and the specific heat capacity are studied. It is found that these materials behave as materials with an internal convectionlike term that provides them with nonreciprocal properties, in the sense that the heat flux has different properties when it propagates in the same direction or in the opposite one to the modulation of the parameters. An effective medium description is presented which accurately describes the modulated material, and numerical simulations support this description and verify the nonreciprocal properties of the material. It is found that these materials are promising candidates for the design of thermal diodes and other advanced devices for the control of the heat flow at all scales.

Atomistic and holistic understanding in physics

International Nuclear Information System (INIS)

Bohm, A.

1992-01-01

Understanding means always reduction to the simpler. In the atomistic understanding the reduction is to the simpler objects. One asks the question: what does it consist of? For instance, one asks: What does the molecule consist of? and the answer is: The molecule consists of electrons and nuclei. Or: what does the nucleus consist of? And the answer is: The nucleus consists of protons and neutrons. The parts in the atomistic understanding are the constituents. In the holistic understanding, the reduction is to the simpler functions, the simpler motions. One asks the question: What does it do? What does the molecule do? What does the nucleus do? And the answer is: The molecule rotates and oscillates. The nucleus rotates and oscillates

Evaluation of spatial and spatiotemporal estimation methods in simulation of precipitation variability patterns

Science.gov (United States)

Bayat, Bardia; Zahraie, Banafsheh; Taghavi, Farahnaz; Nasseri, Mohsen

2013-08-01

Identification of spatial and spatiotemporal precipitation variations plays an important role in different hydrological applications such as missing data estimation. In this paper, the results of Bayesian maximum entropy (BME) and ordinary kriging (OK) are compared for modeling spatial and spatiotemporal variations of annual precipitation with and without incorporating elevation variations. The study area of this research is Namak Lake watershed located in the central part of Iran with an area of approximately 90,000 km2. The BME and OK methods have been used to model the spatial and spatiotemporal variations of precipitation in this watershed, and their performances have been evaluated using cross-validation statistics. The results of the case study have shown the superiority of BME over OK in both spatial and spatiotemporal modes. The results have shown that BME estimates are less biased and more accurate than OK. The improvements in the BME estimates are mostly related to incorporating hard and soft data in the estimation process, which resulted in more detailed and reliable results. Estimation error variance for BME results is less than OK estimations in the study area in both spatial and spatiotemporal modes.

Atomistic approach to predict the glass-forming ability in Zr–Cu–Al ternary metallic glasses

Energy Technology Data Exchange (ETDEWEB)

Yu, C.Y. [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, X.J. [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Zheng, G.P. [Department of Mechanical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong (China); Niu, X.R. [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, C.T., E-mail: chainliu@cityu.edu.hk [Center for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, College of Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong (China)

2015-04-05

Highlights: • An atomistic approach has been developed to predict the glass forming ability (GFA) in Zr–Cu–Al ternary alloy system. • Both of the thermodynamic and structure-dependent kinetic effects to glass formation have been taken into account. • The first-principles calculation and molecular dynamics simulation have been performed. • The approach predicts the best glass former in the model Zr–Cu–Al alloy system. • The predicted GFA is consistent with various experimental results. - Abstract: Prediction of composition-dependent glass-forming ability (GFA) remains to be a key scientific challenge in the metallic-glass community, especially in multi-component alloy systems. In the present study, we apply an atomistic approach to predict the trend of GFA effectively in the Zr–Cu–Al ternary alloy system from alloy compositions alone. This approach is derived from the first-principles calculations based on the density-functional theory and molecular dynamic (MD) simulations. By considering of both the thermodynamic and atomic-structure induced kinetic effects, the predicted GFA trend from this approach shows an excellent agreement with experimental data available in this alloy system, manifesting its capability of seeking metallic glasses with superior GFA in ternary alloy systems.

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations.

Science.gov (United States)

Quevillon, Michael J; Whitmer, Jonathan K

2018-01-02

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure-constant temperature ensemble. These materials exhibit a distinct "smectic" liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications.

Atomistic calculation of size effects on elastic coefficients in nanometre-sized tungsten layers and wires

International Nuclear Information System (INIS)

Villain, P.; Beauchamp, P.; Badawi, K.F.; Goudeau, P.; Renault, P.-O.

2004-01-01

Equilibrium state and elastic coefficients of nanometre-sized single crystal tungsten layers and wires are investigated by atomistic simulations. The variations of the equilibrium distances as a function of the layer thickness or wire cross-section are mainly due to elastic effects of surface tension forces. A strong decrease of the Young's modulus is observed when the transverse dimensions are reduced below 2-3 nm

Large-Scale Covariability Between Aerosol and Precipitation Over the 7-SEAS Region: Observations and Simulations

Science.gov (United States)

Huang, Jingfeng; Hsu, N. Christina; Tsay, Si-Chee; Zhang, Chidong; Jeong, Myeong Jae; Gautam, Ritesh; Bettenhausen, Corey; Sayer, Andrew M.; Hansell, Richard A.; Liu, Xiaohong;

Dynamic decomposition of spatiotemporal neural signals.

Directory of Open Access Journals (Sweden)

Luca Ambrogioni

2017-05-01

Full Text Available Neural signals are characterized by rich temporal and spatiotemporal dynamics that reflect the organization of cortical networks. Theoretical research has shown how neural networks can operate at different dynamic ranges that correspond to specific types of information processing. Here we present a data analysis framework that uses a linearized model of these dynamic states in order to decompose the measured neural signal into a series of components that capture both rhythmic and non-rhythmic neural activity. The method is based on stochastic differential equations and Gaussian process regression. Through computer simulations and analysis of magnetoencephalographic data, we demonstrate the efficacy of the method in identifying meaningful modulations of oscillatory signals corrupted by structured temporal and spatiotemporal noise. These results suggest that the method is particularly suitable for the analysis and interpretation of complex temporal and spatiotemporal neural signals.

Large-scale Validation of AMIP II Land-surface Simulations: Preliminary Results for Ten Models

Energy Technology Data Exchange (ETDEWEB)

Phillips, T J; Henderson-Sellers, A; Irannejad, P; McGuffie, K; Zhang, H

2005-12-01

This report summarizes initial findings of a large-scale validation of the land-surface simulations of ten atmospheric general circulation models that are entries in phase II of the Atmospheric Model Intercomparison Project (AMIP II). This validation is conducted by AMIP Diagnostic Subproject 12 on Land-surface Processes and Parameterizations, which is focusing on putative relationships between the continental climate simulations and the associated models' land-surface schemes. The selected models typify the diversity of representations of land-surface climate that are currently implemented by the global modeling community. The current dearth of global-scale terrestrial observations makes exacting validation of AMIP II continental simulations impractical. Thus, selected land-surface processes of the models are compared with several alternative validation data sets, which include merged in-situ/satellite products, climate reanalyses, and off-line simulations of land-surface schemes that are driven by observed forcings. The aggregated spatio-temporal differences between each simulated process and a chosen reference data set then are quantified by means of root-mean-square error statistics; the differences among alternative validation data sets are similarly quantified as an estimate of the current observational uncertainty in the selected land-surface process. Examples of these metrics are displayed for land-surface air temperature, precipitation, and the latent and sensible heat fluxes. It is found that the simulations of surface air temperature, when aggregated over all land and seasons, agree most closely with the chosen reference data, while the simulations of precipitation agree least. In the latter case, there also is considerable inter-model scatter in the error statistics, with the reanalyses estimates of precipitation resembling the AMIP II simulations more than to the chosen reference data. In aggregate, the simulations of land-surface latent and

Ab-initio and atomistic study of the ferroelectric properties of Cu doped potassium niobate

Energy Technology Data Exchange (ETDEWEB)

Koerbel, Sabine; Elsaesser, Christian [Fraunhofer-Institut fuer Werkstoffmechanik IWM, Woehlerstrasse 11, 79108 Freiburg (Germany)

2011-07-01

KNbO{sub 3} is one end member of the solid solution (K,Na)NbO{sub 3} (KNN), which has promising ferroelectric properties to become a future lead-free substitute for lead zirconate titanate Pb(Zr,Ti)O{sub 3} (PZT) in piezoelectric actors and sensors. Both KNN and PZT exhibit a phase transition with composition and a morphotropic phase boundary, at which enhanced piezoelectric coefficients are obtained. The material properties of PZT and KNN are commonly optimized by doping. E.g., CuO can be added when fabricating KNN as a sintering aid. Ab initio density functional theory and atomistic simulation using a classical shell model potential have been combined to investigate low Cu concentrations in the KNbO{sub 3}-CuNbO{sub 3} system. The atomistic model predicts a morphotropic phase boundary at a few percent Cu, analogous to the one found in the LiNbO{sub 3}-KNbO{sub 3} system.

Probing the limits of metal plasticity with molecular dynamics simulations

Science.gov (United States)

Zepeda-Ruiz, Luis A.; Stukowski, Alexander; Oppelstrup, Tomas; Bulatov, Vasily V.

2017-10-01

Ordinarily, the strength and plasticity properties of a metal are defined by dislocations--line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocation dynamics models are usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive to perform routinely. However, atomistic simulations accurately capture every possible mechanism of material response, resolving every ``jiggle and wiggle'' of atomic motion, whereas dislocation dynamics models do not. Here we present fully dynamic atomistic simulations of bulk single-crystal plasticity in the body-centred-cubic metal tantalum. Our goal is to quantify the conditions under which the limits of dislocation-mediated plasticity are reached and to understand what happens to the metal beyond any such limit. In our simulations, the metal is compressed at ultrahigh strain rates along its [001] crystal axis under conditions of constant pressure, temperature and strain rate. To address the complexity of crystal plasticity processes on the length scales (85-340 nm) and timescales (1 ns-1μs) that we examine, we use recently developed methods of in situ computational microscopy to recast the enormous amount of transient trajectory data generated in our simulations into a form that can be analysed by a human. Our simulations predict that, on reaching certain limiting conditions of strain, dislocations alone can no longer relieve mechanical loads; instead, another mechanism, known as deformation twinning (the sudden re-orientation of the crystal lattice), takes over as the dominant mode of dynamic response. Below this limit, the metal assumes a strain-path-independent steady state of plastic flow in which the flow stress and the dislocation density remain constant as long as the conditions of straining thereafter remain unchanged. In this distinct state, tantalum flows like a viscous fluid while retaining its crystal lattice and remaining a strong

Stearic acid spin labels in lipid bilayers :  insight through atomistic simulations

NARCIS (Netherlands)

Stimson, L.M.; Dong, L.; Karttunen, M.E.J.; Wisniewska, A.; Dutka, M.; Róg, T.

2007-01-01

Spin-labeled stearic acid species are commonly used for electron paramagnetic resonance (EPR) studies of cell membranes to investigate phase transitions, fluidity, and other physical properties. In this paper, we use large-scale molecular dynamics simulations to investigate the position and behavior

Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

Energy Technology Data Exchange (ETDEWEB)

Vögele, Martin [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany); Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M. (Germany); Holm, Christian; Smiatek, Jens, E-mail: smiatek@icp.uni-stuttgart.de [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany)

2015-12-28

We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.

Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

International Nuclear Information System (INIS)

Vögele, Martin; Holm, Christian; Smiatek, Jens

2015-01-01

We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

Science.gov (United States)

Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

2015-10-08

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

Dislocation-stacking fault tetrahedron interaction: what can we learn from atomic-scale modelling

International Nuclear Information System (INIS)

Osetsky, Yu.N.; Stoller, R.E.; Matsukawa, Y.

2004-01-01

The high number density of stacking fault tetrahedra (SFTs) observed in irradiated fcc metals suggests that they should contribute to radiation-induced hardening and, therefore, taken into account when estimating mechanical properties changes of irradiated materials. The central issue is describing the individual interaction between a moving dislocation and an SFT, which is characterized by a very fine size scale, ∼100 nm. This scale is amenable to both in situ TEM experiments and large-scale atomic modelling. In this paper we present results of an atomistic simulation of dislocation-SFT interactions using molecular dynamics (MD). The results are compared with observations from in situ deformation experiments. It is demonstrated that in some cases the simulations and experimental observations are quite similar, suggesting a reasonable interpretation of experimental observations

Spatio-temporal spike train analysis for large scale networks using the maximum entropy principle and Monte Carlo method

International Nuclear Information System (INIS)

Nasser, Hassan; Cessac, Bruno; Marre, Olivier

2013-01-01

Understanding the dynamics of neural networks is a major challenge in experimental neuroscience. For that purpose, a modelling of the recorded activity that reproduces the main statistics of the data is required. In the first part, we present a review on recent results dealing with spike train statistics analysis using maximum entropy models (MaxEnt). Most of these studies have focused on modelling synchronous spike patterns, leaving aside the temporal dynamics of the neural activity. However, the maximum entropy principle can be generalized to the temporal case, leading to Markovian models where memory effects and time correlations in the dynamics are properly taken into account. In the second part, we present a new method based on Monte Carlo sampling which is suited for the fitting of large-scale spatio-temporal MaxEnt models. The formalism and the tools presented here will be essential to fit MaxEnt spatio-temporal models to large neural ensembles. (paper)

Modeling and simulation with operator scaling

OpenAIRE

Cohen, Serge; Meerschaert, Mark M.; Rosiński, Jan

2010-01-01

Self-similar processes are useful in modeling diverse phenomena that exhibit scaling properties. Operator scaling allows a different scale factor in each coordinate. This paper develops practical methods for modeling and simulating stochastic processes with operator scaling. A simulation method for operator stable Levy processes is developed, based on a series representation, along with a Gaussian approximation of the small jumps. Several examples are given to illustrate practical application...

Simulation of Initiation in Hexanitrostilbene

Science.gov (United States)

Thompson, Aidan; Shan, Tzu-Ray; Yarrington, Cole; Wixom, Ryan

We report on the effect of isolated voids and pairs of nearby voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock loading. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating in HNS crystal along the [010] orientation are performed (up = 1.25 km/s, Us =4.0 km/s, P = 11GPa.) We compare the effect on hot spot formation and growth rate of isolated cylindrical voids up to 0.1 µm in size with that of two 50nm voids set 100nm apart. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lock- heed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Physics and performances of III-V nanowire broken-gap heterojunction TFETs using an efficient tight-binding mode-space NEGF model enabling million-atom nanowire simulations.

Science.gov (United States)

Afzalian, A; Vasen, T; Ramvall, P; Shen, T-M; Wu, J; Passlack, M

2018-06-27

We report the capability to simulate in a quantum-mechanical atomistic fashion record-large nanowire devices, featuring several hundred to millions of atoms and a diameter up to 18.2 nm. We have employed a tight-binding mode-space NEGF technique demonstrating by far the fastest (up to 10 000  ×  faster) but accurate (error  <  1%) atomistic simulations to date. Such technique and capability opens new avenues to explore and understand the physics of nanoscale and mesoscopic devices dominated by quantum effects. In particular, our method addresses in an unprecedented way the technologically-relevant case of band-to-band tunneling (BTBT) in III-V nanowire broken-gap heterojunction tunnel-FETs (HTFETs). We demonstrate an accurate match of simulated BTBT currents to experimental measurements in a 12 nm diameter InAs NW and in an InAs/GaSb Esaki tunneling diode. We apply our TB MS simulations and report the first in-depth atomistic study of the scaling potential of III-V GAA nanowire HTFETs including the effect of electron-phonon scattering and discrete dopant impurity band tails, quantifying the benefits of this technology for low-power low-voltage CMOS applications.

Activated states for cross-slip at screw dislocation intersections in face-centered cubic nickel and copper via atomistic simulation

International Nuclear Information System (INIS)

Rao, S.I.; Dimiduk, D.M.; El-Awady, J.A.; Parthasarathy, T.A.; Uchic, M.D.; Woodward, C.

2010-01-01

We extend our recent simulation studies where a screw dislocation in face-centered cubic (fcc) Ni was found to spontaneously attain a low energy partially cross-slipped configuration upon intersecting a forest dislocation. Using atomistic (molecular statics) simulations with embedded atom potentials, we evaluated the activation barrier for a dislocation to transform from fully residing on the glide plane to fully residing on a cross-slip plane intersecting a forest dislocation in both Ni and Cu. The activation energies were obtained by determining equilibrium configurations (energies) when variable pure tensile or compressive stresses were applied along the [1 1 1] direction on the partially cross-slipped state. We show that the activation energy is a factor of 2-5 lower than that for cross-slip in isolation via the Escaig process. The cross-slip activation energies obtained at the intersection in Cu were in reasonable accord with the experimentally determined cross-slip activation energy for Cu. Further, the activation barrier for cross-slip at these intersections was shown to be linearly proportional to (d/b)[ln(√(3)d/b)] 1/2 , as in the Escaig process, where d is the Shockley partial dislocation spacing and b is the Burgers vector of the screw dislocation. These results suggest that cross-slip should be preferentially observed at selected screw dislocation intersections in fcc materials.

Multiscale modeling for ferroelectric materials: identification of the phase-field model’s free energy for PZT from atomistic simulations

International Nuclear Information System (INIS)

Völker, Benjamin; Landis, Chad M; Kamlah, Marc

2012-01-01

Within a knowledge-based multiscale simulation approach for ferroelectric materials, the atomic level can be linked to the mesoscale by transferring results from first-principles calculations into a phase-field model. A recently presented routine (Völker et al 2011 Contin. Mech. Thermodyn. 23 435–51) for adjusting the Helmholtz free energy coefficients to intrinsic and extrinsic ferroelectric material properties obtained by DFT calculations and atomistic simulations was subject to certain limitations: caused by too small available degrees of freedom, an independent adjustment of the spontaneous strains and piezoelectric coefficients was not possible, and the elastic properties could only be considered in cubic instead of tetragonal symmetry. In this work we overcome such restrictions by expanding the formulation of the free energy function, i.e. by motivating and introducing new higher-order terms that have not appeared in the literature before. Subsequently we present an improved version of the adjustment procedure for the free energy coefficients that is solely based on input parameters from first-principles calculations performed by Marton and Elsässer, as documented in Völker et al (2011 Contin. Mech. Thermodyn. 23 435–51). Full sets of adjusted free energy coefficients for PbTiO 3 and tetragonal Pb(Zr,Ti)O 3 are presented, and the benefits of the newly introduced higher-order free energy terms are discussed. (paper)

Time-Domain Ab Initio Analysis of Excitation Dynamics in a Quantum Dot/Polymer Hybrid: Atomistic Description Rationalizes Experiment.

Science.gov (United States)

Long, Run; Prezhdo, Oleg V

2015-07-08

Hybrid organic/inorganic polymer/quantum dot (QD) solar cells are an attractive alternative to the traditional cells. The original, simple models postulate that one-dimensional polymers have continuous energy levels, while zero-dimensional QDs exhibit atom-like electronic structure. A realistic, atomistic viewpoint provides an alternative description. Electronic states in polymers are molecule-like: finite in size and discrete in energy. QDs are composed of many atoms and have high, bulk-like densities of states. We employ ab initio time-domain simulation to model the experimentally observed ultrafast photoinduced dynamics in a QD/polymer hybrid and show that an atomistic description is essential for understanding the time-resolved experimental data. Both electron and hole transfers across the interface exhibit subpicosecond time scales. The interfacial processes are fast due to strong electronic donor-acceptor, as evidenced by the densities of the photoexcited states which are delocalized between the donor and the acceptor. The nonadiabatic charge-phonon coupling is also strong, especially in the polymer, resulting in rapid energy losses. The electron transfer from the polymer is notably faster than the hole transfer from the QD, due to a significantly higher density of acceptor states. The stronger molecule-like electronic and charge-phonon coupling in the polymer rationalizes why the electron-hole recombination inside the polymer is several orders of magnitude faster than in the QD. As a result, experiments exhibit multiple transfer times for the long-lived hole inside the QD, ranging from subpicoseconds to nanoseconds. In contrast, transfer of the short-lived electron inside the polymer does not occur beyond the first picosecond. The energy lost by the hole on its transit into the polymer is accommodated by polymer's high-frequency vibrations. The energy lost by the electron injected into the QD is accommodated primarily by much lower-frequency collective and

Analysis and modelling of spatio-temporal properties of daily rainfall over the Danube basin

Science.gov (United States)

Serinaldi, F.; Kilsby, C. G.

2012-04-01

Central and Eastern Europe are prone to severe floods due to heavy rainfall that cause societal and economic damages, ranging from agriculture to water resources, from the insurance/reinsurance sector to the energy industry. To improve the flood risk analysis, a better characterisation and modelling of the rainfall patterns over this area, which involves the Danube river watershed, is strategically important. In this study, we analyse the spatio-temporal properties of a large data set of daily rainfall time series from 15 countries in the Central Eastern Europe through different lagged and non-lagged indices of associations that quantify both the overall dependence and extreme dependence of pairwise observations. We also show that these measures are linked to each other and can be written in a unique and coherent notation within the copula framework. Moreover, the lagged version of these measures allows exploring some important spatio-temporal properties of the rainfall fields. The exploratory analysis is complemented by the preliminary results of a spatio-temporal rainfall simulation performed via a compound model based upon the Generalized Additive Models for Location, Scale and Shape (GAMLSS) and meta-elliptical multivariate distributions.

Multiscale recurrence analysis of spatio-temporal data

Science.gov (United States)

Riedl, M.; Marwan, N.; Kurths, J.

2015-12-01

The description and analysis of spatio-temporal dynamics is a crucial task in many scientific disciplines. In this work, we propose a method which uses the mapogram as a similarity measure between spatially distributed data instances at different time points. The resulting similarity values of the pairwise comparison are used to construct a recurrence plot in order to benefit from established tools of recurrence quantification analysis and recurrence network analysis. In contrast to other recurrence tools for this purpose, the mapogram approach allows the specific focus on different spatial scales that can be used in a multi-scale analysis of spatio-temporal dynamics. We illustrate this approach by application on mixed dynamics, such as traveling parallel wave fronts with additive noise, as well as more complicate examples, pseudo-random numbers and coupled map lattices with a semi-logistic mapping rule. Especially the complicate examples show the usefulness of the multi-scale consideration in order to take spatial pattern of different scales and with different rhythms into account. So, this mapogram approach promises new insights in problems of climatology, ecology, or medicine.

From empirical to ab initio: transferable potentials in the atomistic simulation of amorphous carbons

International Nuclear Information System (INIS)

Marks, N.A.; Goringe, C.M.; McKenzie, D.R.; McCulloch, D.G.; Royal Melbourne Institute of Technology University, Melbourne, VIC

2000-01-01

Full text: Silicon is often described as the prototype covalent material, and when it comes to developing atomistic models this situation is well described by the sentiment that 'everything works for silicon'. The same cannot be said for carbon though, where the interaction potential has always proved problematical, be it with empirical, tight-binding or ab initio methods. Thus far the most decisive contributions to understanding amorphous carbon networks have come from ab initio simulations using the Car-Parrinello method, where the fully quantum treatment of the valence electrons has provided unexpected insight into the local structure. However such first principles calculations are restricted spatially and temporally to systems with approximately 100 atoms and times of order one picosecond. There is therefore demand for less expensive techniques capable of resolving important questions whose solution can only to found with larger simulations running for longer times. In the case of tetrahedral amorphous carbon, such issues include the release of compressive stress through annealing, the origin of graphitic surface layers and the nature of the film growth process and thermal spike. Against this background tight-binding molecular dynamics has emerged as a popular alternative to first principles methods, and our group has an ongoing program to understand film growth using one of the efficient variants of tight-binding. Another direction of research is a new empirical potential based on the Environment Dependent Interaction Potential (EDIP) recently developed for silicon. The EDIP approach represents a promising direction for empirical potentials through its use of ab initio data to motivate the functional form as well as the more conventional parametrisation. By inverting ab initio cohesive energy curves the authors of EDIP arrived at a pair potential expression which reduces to the well-known Stillinger-Weber form at integer coordination, while providing

Deformation behavior of Cu bicrystals with the Σ9(110)(221) symmetric tilt grain boundary under pure shear studied by atomistic simulation method

International Nuclear Information System (INIS)

Wan Liang; Wang Shaoqing

2010-01-01

The deformation behavior of Cu bicrystals with the symmetric tilt grain boundary (STGB) under pure shear has been studied by atomistic simulation method with the embedded atom method (EAM) interatomic potentials. By using an energy minimization method, it shows that there are two optimized structures of this grain boundary (GB) which correspond to two local energy minima on the potential energy surface of the GB. The structure with lower energy is the stable one while the other is a metastable structure. The pure shear process of the bicrystals at ambient temperature has been studied by molecular dynamics (MD) simulation method. The simulated results indicate that there are three structure transformation modes of this GB depending on the shear direction: (1) pure GB sliding; (2) GB atomic shuffling accompanied by dislocation emission from GB; (3) GB migration coupled GB sliding, namely, GB coupling motion. In addition, an analysis of the structure evolution of the GB shows that, there are two mechanisms for GB coupling motion depending on the shear direction. One is the collective motion of GB atoms and the other is structure transformation realized by uncorrelated atomic shuffling processes. The former mechanism can induce structure transition of GB between the stable one and the metastable one, while the latter introduces faceting of the GB. (authors)

Atomistic switch of giant magnetoresistance and spin thermopower in graphene-like nanoribbons

Science.gov (United States)

Zhai, Ming-Xing; Wang, Xue-Feng

2016-01-01

We demonstrate that the giant magnetoresistance can be switched off (on) in even- (odd-) width zigzag graphene-like nanoribbons by an atomistic gate potential or edge disorder inside the domain wall in the antiparallel (ap) magnetic configuration. A strong magneto-thermopower effect is also predicted that the spin thermopower can be greatly enhanced in the ap configuration while the charge thermopower remains low. The results extracted from the tight-binding model agree well with those obtained by first-principles simulations for edge doped graphene nanoribbons. Analytical expressions in the simplest case are obtained to facilitate qualitative analyses in general contexts. PMID:27857156

Dynamical topology and statistical properties of spatiotemporal chaos.

Science.gov (United States)

Zhuang, Quntao; Gao, Xun; Ouyang, Qi; Wang, Hongli

2012-12-01

For spatiotemporal chaos described by partial differential equations, there are generally locations where the dynamical variable achieves its local extremum or where the time partial derivative of the variable vanishes instantaneously. To a large extent, the location and movement of these topologically special points determine the qualitative structure of the disordered states. We analyze numerically statistical properties of the topologically special points in one-dimensional spatiotemporal chaos. The probability distribution functions for the number of point, the lifespan, and the distance covered during their lifetime are obtained from numerical simulations. Mathematically, we establish a probabilistic model to describe the dynamics of these topologically special points. In spite of the different definitions in different spatiotemporal chaos, the dynamics of these special points can be described in a uniform approach.

Atomistic computer simulations on multi-loaded PAMAM dendrimers: a comparison of amine- and hydroxyl-terminated dendrimers

Science.gov (United States)

Badalkhani-Khamseh, Farideh; Ebrahim-Habibi, Azadeh; Hadipour, Nasser L.

2017-12-01

Poly(amidoamine) (PAMAM) dendrimers have been extensively studied as delivery vectors in biomedical applications. A limited number of molecular dynamics (MD) simulation studies have investigated the effect of surface chemistry on therapeutic molecules loading, with the aim of providing insights for biocompatibility improvement and increase in drug loading capacity of PAMAM dendrimers. In this work, fully atomistic MD simulations were employed to study the association of 5-Fluorouracil (5-FU) with amine (NH2)- and hydroxyl (OH)-terminated PAMAM dendrimers of generations 3 and 4 (G3 and G4). MD results show a 1:12, 1:1, 1:27, and 1:4 stoichiometry, respectively, for G3NH2-FU, G3OH-FU, G4NH2-FU, and G4OH-FU complexes, which is in good agreement with the isothermal titration calorimetry results. The results obtained showed that NH2-terminated dendrimers assume segmented open structures with large cavities and more drug molecules can encapsulate inside the dendritic cavities of amine terminated dendrimers. However, OH-terminated have a densely packed structure and therefore, 5-FU drug molecules are more stable to locate close to the surface of the dendrimers. Intermolecular hydrogen bonding analysis showed that 5-FU drug molecules have more tendency to form hydrogen bonds with terminal monomers of OH-terminated dendrimers, while in NH2-terminated these occur both in the inner region and the surface. Furthermore, MM-PBSA analysis revealed that van der Waals and electrostatic energies are both important to stabilize the complexes. We found that drug molecules are distributed uniformly inside the amine and hydroxyl terminated dendrimers and therefore, both dendrimers are promising candidates as drug delivery systems for 5-FU drug molecules.

Atomistic study of lipid membranes containing chloroform: looking for a lipid-mediated mechanism of anesthesia.

Directory of Open Access Journals (Sweden)

Ramon Reigada

Full Text Available The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic and carbon tetrachloride (non-anesthetic. Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.

Visualization of Spatio-Temporal Relations in Movement Event Using Multi-View

Science.gov (United States)

Zheng, K.; Gu, D.; Fang, F.; Wang, Y.; Liu, H.; Zhao, W.; Zhang, M.; Li, Q.

2017-09-01

Spatio-temporal relations among movement events extracted from temporally varying trajectory data can provide useful information about the evolution of individual or collective movers, as well as their interactions with their spatial and temporal contexts. However, the pure statistical tools commonly used by analysts pose many difficulties, due to the large number of attributes embedded in multi-scale and multi-semantic trajectory data. The need for models that operate at multiple scales to search for relations at different locations within time and space, as well as intuitively interpret what these relations mean, also presents challenges. Since analysts do not know where or when these relevant spatio-temporal relations might emerge, these models must compute statistical summaries of multiple attributes at different granularities. In this paper, we propose a multi-view approach to visualize the spatio-temporal relations among movement events. We describe a method for visualizing movement events and spatio-temporal relations that uses multiple displays. A visual interface is presented, and the user can interactively select or filter spatial and temporal extents to guide the knowledge discovery process. We also demonstrate how this approach can help analysts to derive and explain the spatio-temporal relations of movement events from taxi trajectory data.

VISUALIZATION OF SPATIO-TEMPORAL RELATIONS IN MOVEMENT EVENT USING MULTI-VIEW

Directory of Open Access Journals (Sweden)

K. Zheng

2017-09-01

Full Text Available Spatio-temporal relations among movement events extracted from temporally varying trajectory data can provide useful information about the evolution of individual or collective movers, as well as their interactions with their spatial and temporal contexts. However, the pure statistical tools commonly used by analysts pose many difficulties, due to the large number of attributes embedded in multi-scale and multi-semantic trajectory data. The need for models that operate at multiple scales to search for relations at different locations within time and space, as well as intuitively interpret what these relations mean, also presents challenges. Since analysts do not know where or when these relevant spatio-temporal relations might emerge, these models must compute statistical summaries of multiple attributes at different granularities. In this paper, we propose a multi-view approach to visualize the spatio-temporal relations among movement events. We describe a method for visualizing movement events and spatio-temporal relations that uses multiple displays. A visual interface is presented, and the user can interactively select or filter spatial and temporal extents to guide the knowledge discovery process. We also demonstrate how this approach can help analysts to derive and explain the spatio-temporal relations of movement events from taxi trajectory data.

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II

Science.gov (United States)

Limmer, David T.; Chandler, David

2013-06-01

This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys. 135, 134503 (2011), 10.1063/1.3643333 and preprint arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light.

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II

International Nuclear Information System (INIS)

Limmer, David T.; Chandler, David

2013-01-01

This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys.135, 134503 (2011) and preprint http://arxiv.org/abs/arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II

Energy Technology Data Exchange (ETDEWEB)

Limmer, David T.; Chandler, David, E-mail: chandler@berkeley.edu [Department of Chemistry, University of California, Berkeley, California 94720 (United States)

2013-06-07

This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys.135, 134503 (2011) and preprint http://arxiv.org/abs/arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light.

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II.

Science.gov (United States)

Limmer, David T; Chandler, David

2013-06-07

This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys. 135, 134503 (2011) and preprint arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light.

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

Science.gov (United States)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

Adjusted functional boxplots for spatio-temporal data visualization and outlier detection

KAUST Repository

Sun, Ying

2011-10-24

This article proposes a simulation-based method to adjust functional boxplots for correlations when visualizing functional and spatio-temporal data, as well as detecting outliers. We start by investigating the relationship between the spatio-temporal dependence and the 1.5 times the 50% central region empirical outlier detection rule. Then, we propose to simulate observations without outliers on the basis of a robust estimator of the covariance function of the data. We select the constant factor in the functional boxplot to control the probability of correctly detecting no outliers. Finally, we apply the selected factor to the functional boxplot of the original data. As applications, the factor selection procedure and the adjusted functional boxplots are demonstrated on sea surface temperatures, spatio-temporal precipitation and general circulation model (GCM) data. The outlier detection performance is also compared before and after the factor adjustment. © 2011 John Wiley & Sons, Ltd.

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)

2015-12-07

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

International Nuclear Information System (INIS)

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

2015-01-01

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level

Spatiotemporal Wave Patterns: Information Dynamics

Energy Technology Data Exchange (ETDEWEB)

Mikhail Rabinovich; Lev Tsimring

2006-01-20

Pattern formation has traditionally been studied in non-equilibrium physics from the viewpoint of describing the basic structures and their interactions. While this is still an important area of research, the emphasis in the last few years has shifted towards analysis of specific properties of patterns in various complex media. For example, diverse and unexpected phenomena occur in neuro-like media that are characterized by highly non-trivial local dynamics. We carried out an active research program on analysis of spatio-temporal patterns in various physical systems (convection, oscillating fluid layer, soap film), as well as in neuro-like media, with an emphasis on informational aspects of the dynamics. Nonlinear nonequilibrium media and their discrete analogs have a unique ability to represent, memorize, and process the information contained in spatio-temporal patterns. Recent neurophysiological experiments demonstrated a certain universality of spatio-temporal representation of information by neural ensembles. Information processing is also revealed in the spatio-temporal dynamics of cellular patterns in nonequilibrium media. It is extremely important for many applications to study the informational aspects of these dynamics, including the origins and mechanisms of information generation, propagation and storage. Some of our results are: the discovery of self-organization of periodically oscillatory patterns in chaotic heterogeneous media; the analysis of the propagation of the information along a chaotic media as function of the entropy of the signal; the analysis of wave propagation in discrete non-equilibrium media with autocatalytic properties, which simulates the calcium dynamics in cellular membranes. Based on biological experiments we suggest the mechanism by which the spatial sensory information is transferred into the spatio-temporal code in the neural media. We also found a new mechanism of self-pinning in cellular structures and the related phenomenon

Fluctuating hydrodynamics for multiscale modeling and simulation: energy and heat transfer in molecular fluids.

Science.gov (United States)

Shang, Barry Z; Voulgarakis, Nikolaos K; Chu, Jhih-Wei

2012-07-28

This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.

Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

International Nuclear Information System (INIS)

Nishizawa, Manami; Nishizawa, Kazuhisa

2014-01-01

Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT OPLS ). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT OPLS PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT CHARMM ) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16–22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT OPLS PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA) 3 peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These findings may help interpret

Atomistic Force Field for Pyridinium-Based Ionic Liquids: Reliable Transport Properties

DEFF Research Database (Denmark)

Voroshylova, I. V.; Chaban, V. V.

2014-01-01

Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)......Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis......(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cationanion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove...... and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia LopesPadua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids....

Visualization and assessment of spatio-temporal covariance properties

KAUST Repository

Huang, Huang

2017-11-23

Spatio-temporal covariances are important for describing the spatio-temporal variability of underlying random fields in geostatistical data. For second-order stationary random fields, there exist subclasses of covariance functions that assume a simpler spatio-temporal dependence structure with separability and full symmetry. However, it is challenging to visualize and assess separability and full symmetry from spatio-temporal observations. In this work, we propose a functional data analysis approach that constructs test functions using the cross-covariances from time series observed at each pair of spatial locations. These test functions of temporal lags summarize the properties of separability or symmetry for the given spatial pairs. We use functional boxplots to visualize the functional median and the variability of the test functions, where the extent of departure from zero at all temporal lags indicates the degree of non-separability or asymmetry. We also develop a rank-based nonparametric testing procedure for assessing the significance of the non-separability or asymmetry. Essentially, the proposed methods only require the analysis of temporal covariance functions. Thus, a major advantage over existing approaches is that there is no need to estimate any covariance matrix for selected spatio-temporal lags. The performances of the proposed methods are examined by simulations with various commonly used spatio-temporal covariance models. To illustrate our methods in practical applications, we apply it to real datasets, including weather station data and climate model outputs.

A Multiphysics Framework to Learn and Predict in Presence of Multiple Scales

Science.gov (United States)

Tomin, P.; Lunati, I.

2015-12-01

Modeling complex phenomena in the subsurface remains challenging due to the presence of multiple interacting scales, which can make it impossible to focus on purely macroscopic phenomena (relevant in most applications) and neglect the processes at the micro-scale. We present and discuss a general framework that allows us to deal with the situation in which the lack of scale separation requires the combined use of different descriptions at different scale (for instance, a pore-scale description at the micro-scale and a Darcy-like description at the macro-scale) [1,2]. The method is based on conservation principles and constructs the macro-scale problem by numerical averaging of micro-scale balance equations. By employing spatiotemporal adaptive strategies, this approach can efficiently solve large-scale problems [2,3]. In addition, being based on a numerical volume-averaging paradigm, it offers a tool to illuminate how macroscopic equations emerge from microscopic processes, to better understand the meaning of microscopic quantities, and to investigate the validity of the assumptions routinely used to construct the macro-scale problems. [1] Tomin, P., and I. Lunati, A Hybrid Multiscale Method for Two-Phase Flow in Porous Media, Journal of Computational Physics, 250, 293-307, 2013 [2] Tomin, P., and I. Lunati, Local-global splitting and spatiotemporal-adaptive Multiscale Finite Volume Method, Journal of Computational Physics, 280, 214-231, 2015 [3] Tomin, P., and I. Lunati, Spatiotemporal adaptive multiphysics simulations of drainage-imbibition cycles, Computational Geosciences, 2015 (under review)

Simulated x-ray scattering of protein solutions using explicit-solvent models

International Nuclear Information System (INIS)

Park, Sanghyun; Bardhan, Jaydeep P.; Makowski, Lee; Roux, Benoit

2009-01-01

X-ray solution scattering shows new promise for the study of protein structures, complementing crystallography and nuclear magnetic resonance. In order to realize the full potential of solution scattering, it is necessary to not only improve experimental techniques but also develop accurate and efficient computational schemes to relate atomistic models to measurements. Previous computational methods, based on continuum models of water, have been unable to calculate scattering patterns accurately, especially in the wide-angle regime which contains most of the information on the secondary, tertiary, and quaternary structures. Here we present a novel formulation based on the atomistic description of water, in which scattering patterns are calculated from atomic coordinates of protein and water. Without any empirical adjustments, this method produces scattering patterns of unprecedented accuracy in the length scale between 5 and 100 A, as we demonstrate by comparing simulated and observed scattering patterns for myoglobin and lysozyme.

Investigation of the removing process of cathode material in micro-EDM using an atomistic-continuum model

International Nuclear Information System (INIS)

Guo, Jianwen; Zhang, Guojun; Huang, Yu; Ming, Wuyi; Liu, Min; Huang, Hao

2014-01-01

Highlights: • An atomistic-continuum computational simulation model for single-discharge micro-EDM process of Cu cathode is constructed. • Cathode material is removed mainly in the form of single atoms or small clusters in micro-EDM. • Electric action leads to the formation of peaks on the surface of crater. • Removing process of cathode material under the hybrid action combining the thermal action and the electric action is studied, and the strength of either action needed for material to remove is much reduced. - Abstract: In micro-electrical discharge machining (micro-EDM), the discharge duration is ultra-short, and both the electric action and the thermal action by the discharge channel play important roles in the removing process of cathode material. However, in most researches on the machining mechanism of micro-EDM, only the thermal action is concerned. In this article, a combined atomistic-continuum modeling method in which the two-temperature model and the molecular dynamics simulation model are integrated is used to construct the simulation model for cathode in single-discharge micro-EDM process. With this simulation model, removing processes of Cu cathode material in micro-EDM under pure thermal action, pure electric action and the combination of them are investigated in a simulative way. By analyzing evolutions of temperature, stress and micro-structure of material as well as the dynamical behaviors of material in the removing process, mechanisms of the cathode material removal and crater formation are revealed. In addition, the removing process of cathode material under the combination of pure thermal action and pure electric action is compared with those under the two pure actions respectively to analyze the interactive effect between the thermal action and the electric action

Structure of Cu64.5Zr35.5 metallic glass by reverse Monte Carlo simulations

International Nuclear Information System (INIS)

Fang, X. W.; Huang, Li; Wang, C. Z.; Ho, K. M.; Ding, Z. J.

2014-01-01

Reverse Monte Carlo simulations (RMC) have been widely used to generate three dimensional (3D) atomistic models for glass systems. To examine the reliability of the method for metallic glass, we use RMC to predict the atomic configurations of a “known” structure from molecular dynamics (MD) simulations, and then compare the structure obtained from the RMC with the target structure from MD. We show that when the structure factors and partial pair correlation functions from the MD simulations are used as inputs for RMC simulations, the 3D atomistic structure of the glass obtained from the RMC gives the short- and medium-range order in good agreement with those from the target structure by the MD simulation. These results suggest that 3D atomistic structure model of the metallic glass alloys can be reasonably well reproduced by RMC method with a proper choice of input constraints

Investigating dislocation motion through a field of solutes with atomistic simulations and reaction rate theory

International Nuclear Information System (INIS)

Saroukhani, S.; Warner, D.H.

2017-01-01

The rate of thermally activated dislocation motion across a field of solutes is studied using traditional and modern atomistically informed rate theories. First, the accuracy of popular variants of the Harmonic Transition State Theory, as the most common approach, is examined by comparing predictions to direct MD simulations. It is shown that HTST predictions are grossly inaccurate due to the anharmonic effect of thermal softening. Next, the utility of the Transition Interface Sampling was examined as the method was recently shown to be effective for predicting the rate of dislocation-precipitate interactions. For dislocation-solute interactions studied here, TIS is found to be accurate only when the dislocation overcomes multiple obstacles at a time, i.e. jerky motion, and it is inaccurate in the unpinning regime where the energy barrier is of diffusive nature. It is then shown that the Partial Path TIS method - designed for diffusive barriers - provides accurate predictions in the unpinning regime. The two methods are then used to study the temperature and load dependence of the rate. It is shown that Meyer-Neldel (MN) rule prediction of the entropy barrier is not as accurate as it is in the case of dislocation-precipitate interactions. In response, an alternative model is proposed that provides an accurate prediction of the entropy barrier. This model can be combined with TST to offer an attractively simple rate prediction approach. Lastly, (PP)TIS is used to predict the Strain Rate Sensitivity (SRS) factor at experimental strain rates and the predictions are compared to experimental values.

Atomistic modelling of diffusional phase transformations with elastic strain

International Nuclear Information System (INIS)

Mason, D R; Rudd, R E; Sutton, A P

2004-01-01

Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Atomic interactions are modelled by Finnis-Sinclair potentials constructed for these simulations. Vacancy diffusion is modelled by comparing the energies of trial states, where the system is partially relaxed for each trial state. No special requirements are made about the description of atomic interactions, making our approach suitable for more fundamentally based models such as tight binding if sufficient computational resources are available. Only a limited precision is required for the energy of each trial state, determined by the value of k B T. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r 3 , it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centred on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice

Atomistic simulation on charge mobility of amorphous tris(8-hydroxyquinoline) aluminum (Alq3): origin of Poole-Frenkel-type behavior.

Science.gov (United States)

Nagata, Yuki; Lennartz, Christian

2008-07-21

The atomistic simulation of charge transfer process for an amorphous Alq(3) system is reported. By employing electrostatic potential charges, we calculate site energies and find that the standard deviation of site energy distribution is about twice as large as predicted in previous research. The charge mobility is calculated via the Miller-Abrahams formalism and the master equation approach. We find that the wide site energy distribution governs Poole-Frenkel-type behavior of charge mobility against electric field, while the spatially correlated site energy is not a dominant mechanism of Poole-Frenkel behavior in the range from 2x10(5) to 1.4x10(6) V/cm. Also we reveal that randomly meshed connectivities are, in principle, required to account for the Poole-Frenkel mechanism. Charge carriers find a zigzag pathway at low electric field, while they find a straight pathway along electric field when a high electric field is applied. In the space-charge-limited current scheme, the charge-carrier density increases with electric field strength so that the nonlinear behavior of charge mobility is enhanced through the strong charge-carrier density dependence of charge mobility.

Molecular dynamics simulations of stratum corneum lipid mixtures: A multiscale perspective.

Science.gov (United States)

Moore, Timothy C; Iacovella, Christopher R; Leonhard, Anne C; Bunge, Annette L; McCabe, Clare

2018-03-29

The lipid matrix of the stratum corneum (SC) layer of skin is essential for human survival; it acts as a barrier to prevent rapid dehydration while keeping potentially hazardous material outside the body. While the composition of the SC lipid matrix is known, the molecular-level details of its organization are difficult to infer experimentally, hindering the discovery of structure-property relationships. To this end, molecular dynamics simulations, which give molecular-level resolution, have begun to play an increasingly important role in understanding these relationships. However, most simulation studies of SC lipids have focused on preassembled bilayer configurations, which, owing to the slow dynamics of the lipids, may influence the final structure and hence the calculated properties. Self-assembled structures would avoid this dependence on the initial configuration, however, the size and length scales involved make self-assembly impractical to study with atomistic models. Here, we report on the development of coarse-grained models of SC lipids designed to study self-assembly. Building on previous work, we present the interactions between the headgroups of ceramide and free fatty acid developed using the multistate iterative Boltzmann inversion method. Validation of the new interactions is performed with simulations of preassembled bilayers and good agreement between the atomistic and coarse-grained models is found for structural properties. The self-assembly of mixtures of ceramide and free fatty acid is investigated and both bilayer and multilayer structures are found to form. This work therefore represents a necessary step in studying SC lipid systems on multiple time and length scales. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular dynamics simulations of the atomistic structure of the intergranular film between silicon nitride grains: Effect of composition, thickness, and surface vacancies

International Nuclear Information System (INIS)

Garofalini, Stephen H.

2006-01-01

Molecular dynamics computer simulations were used to study the atomistic structure of intergranular films (IGFs) between two basal oriented Si 3 N 4 crystals or between combined basal and prism oriented crystals. Ordering of the ions into the IGF induced by the crystal surfaces was observed using density profiles of the ions, although that ordering is effected by the roughness of the crystal surface. Density profiles of the sum of all ions misleadingly shows a rapid decay in the density oscillations and apparent ordering into the IGF. However, this is an artifact of the coincidence of the maximum in the peaks of one species with the minimum of another species and the actual oscillations of individual species extend into the IGF farther than the sum profile indicates. This result would have important implications regarding the density oscillations observed in physical experiments with regard to the actual extent of ordering into the IGF induced by the crystal surface

Cationic Dimyristoylphosphatidylcholine and Dioleoyloxytrimethylammonium Propane Lipid Bilayers: Atomistic Insight for Structure and Dynamics

DEFF Research Database (Denmark)

Zhao, W.; Gurtovenko, A. A.; Vattulainen, I.

2012-01-01

We performed atomistic molecular dynamics simulations of lipid bilayers consisting of a mixture of cationic dioleoyloxytrimethylammonium propane (DOTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC) lipids at different DOTAP fractions. Our primary focus was the specific effects...... of unsaturated lipid chains on structural and dynamic properties of mixed cationic bilayers. The bilayer area, as well as the ordering of lipid tails, shows a pronounced nonmonotonic behavior when TAP lipid fraction increases. The minimum in area (maximum in ordering) was observed for a bilayer with TAP fraction...... lipids, which were found to form PC-PC and PC-TAP pairs, and the formation of lipid clusters....

Atomistic modeling of defect evolution in Si for amorphizing and subamorphizing implants

International Nuclear Information System (INIS)

Lopez, Pedro; Pelaz, Lourdes; Marques, Luis A.; Santos, Ivan; Aboy, Maria; Barbolla, Juan

2004-01-01

Solid phase epitaxial regrowth of pre-amorphizing implants has received significant attention as a method to achieve high dopant activation with minimal diffusion at low implant temperatures and suppress channelling. Therefore, a good understanding of the amorphization and regrowth mechanisms is required in process simulators. We present an atomistic amorphization and recrystallization model that uses the interstitial-vacancy (I-V) pair as a building block to describe the amorphous phase. I-V pairs are locally characterized by the number of neighbouring I-V pairs. This feature captures the damage generation and the dynamical annealing during ion implantation, and also explains the annealing behaviour of amorphous layers and amorphous pockets

Experimentally driven atomistic model of 1,2 polybutadiene

Energy Technology Data Exchange (ETDEWEB)

Gkourmpis, Thomas, E-mail: thomas.gkourmpis@borealisgroup.com [Polymer Science Centre, J. J. Thomson Physical Laboratory, Department of Physics, University of Reading, Reading RG6 6AF (United Kingdom); Mitchell, Geoffrey R. [Polymer Science Centre, J. J. Thomson Physical Laboratory, Department of Physics, University of Reading, Reading RG6 6AF (United Kingdom); Centre for Rapid and Sustainable Product Development, Institute Polytechnic Leiria, Marinha Grande (Portugal)

2014-02-07

We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120–400 K. Analysis of the experimental data yields bond lengths for Cî—¸C and C î—» C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.

Visual search of cyclic spatio-temporal events

Science.gov (United States)

Gautier, Jacques; Davoine, Paule-Annick; Cunty, Claire

2018-05-01

The analysis of spatio-temporal events, and especially of relationships between their different dimensions (space-time-thematic attributes), can be done with geovisualization interfaces. But few geovisualization tools integrate the cyclic dimension of spatio-temporal event series (natural events or social events). Time Coil and Time Wave diagrams represent both the linear time and the cyclic time. By introducing a cyclic temporal scale, these diagrams may highlight the cyclic characteristics of spatio-temporal events. However, the settable cyclic temporal scales are limited to usual durations like days or months. Because of that, these diagrams cannot be used to visualize cyclic events, which reappear with an unusual period, and don't allow to make a visual search of cyclic events. Also, they don't give the possibility to identify the relationships between the cyclic behavior of the events and their spatial features, and more especially to identify localised cyclic events. The lack of possibilities to represent the cyclic time, outside of the temporal diagram of multi-view geovisualization interfaces, limits the analysis of relationships between the cyclic reappearance of events and their other dimensions. In this paper, we propose a method and a geovisualization tool, based on the extension of Time Coil and Time Wave, to provide a visual search of cyclic events, by allowing to set any possible duration to the diagram's cyclic temporal scale. We also propose a symbology approach to push the representation of the cyclic time into the map, in order to improve the analysis of relationships between space and the cyclic behavior of events.

Towards a physically-based multi-scale ecohydrological simulator for semi-arid regions

Science.gov (United States)

Caviedes-Voullième, Daniel; Josefik, Zoltan; Hinz, Christoph

2017-04-01

The use of numerical models as tools for describing and understanding complex ecohydrological systems has enabled to test hypothesis and propose fundamental, process-based explanations of the system system behaviour as a whole as well as its internal dynamics. Reaction-diffusion equations have been used to describe and generate organized pattern such as bands, spots, and labyrinths using simple feedback mechanisms and boundary conditions. Alternatively, pattern-matching cellular automaton models have been used to generate vegetation self-organization in arid and semi-arid regions also using simple description of surface hydrological processes. A key question is: How much physical realism is needed in order to adequately capture the pattern formation processes in semi-arid regions while reliably representing the water balance dynamics at the relevant time scales? In fact, redistribution of water by surface runoff at the hillslope scale occurs at temporal resolution of minutes while the vegetation development requires much lower temporal resolution and longer times spans. This generates a fundamental spatio-temporal multi-scale problem to be solved, for which high resolution rainfall and surface topography are required. Accordingly, the objective of this contribution is to provide proof-of-concept that governing processes can be described numerically at those multiple scales. The requirements for a simulating ecohydrological processes and pattern formation with increased physical realism are, amongst others: i. high resolution rainfall that adequately captures the triggers of growth as vegetation dynamics of arid regions respond as pulsed systems. ii. complex, natural topography in order to accurately model drainage patterns, as surface water redistribution is highly sensitive to topographic features. iii. microtopography and hydraulic roughness, as small scale variations do impact on large scale hillslope behaviour iv. moisture dependent infiltration as temporal

Impact of amphiphilic molecules on the structure and stability of homogeneous sphingomyelin bilayer: Insights from atomistic simulations

Science.gov (United States)

Kumari, Pratibha; Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K.

2018-04-01

Modulation of lipid membrane properties due to the permeation of amphiphiles is an important biological process pertaining to many applications in the field of pharmaceutics, toxicology, and biotechnology. Sphingolipids are both structural and functional lipids that constitute an important component of mechanically stable and chemically resistant outer leaflets of plasma membranes. Here, we present an atomistic molecular dynamics simulation study to appreciate the concentration-dependent effects of small amphiphilic molecules, such as ethanol, acetone, and dimethyl sulfoxide (DMSO), on the structure and stability of a fully hydrated homogeneous N-palmitoyl-sphingomyelin (PSM) bilayer. The study reveals an increase in the lateral expansion of the bilayer along with disordering of the hydrophobic lipid tails on increasing the concentration of ethanol. At higher concentrations of ethanol, rupturing of the bilayer is quite evident through the analysis of partial electron density profiles and lipid tail order parameters. For ethanol containing systems, permeation of water molecules in the hydrophobic part of the bilayer is allowed through local defects made due to the entry of ethanol molecules via ethanol-ethanol and ethanol-PSM hydrogen bonds. Moreover, the extent of PSM-PSM hydrogen bonding decreases with increasing ethanol concentration. On the other hand, acetone and DMSO exhibit minimal effects on the stability of the PSM bilayer at their lower concentrations, but at higher concentrations they tend to enhance the stability of the bilayer. The simulated potential of mean force (PMF) profiles for the translocation of the three solutes studied reveal that the free-energy of transfer of an ethanol molecule across the PSM lipid head region is lower than that for acetone and DMSO molecules. However, highest free-energy rise in the core hydrophobic part of the bilayer is observed for the DMSO molecule, whereas the ethanol and acetone PMF profiles show a lower barrier in

On the expected value and variance for an estimator of the spatio-temporal product density function

DEFF Research Database (Denmark)

Rodríguez-Corté, Francisco J.; Ghorbani, Mohammad; Mateu, Jorge

Second-order characteristics are used to analyse the spatio-temporal structure of the underlying point process, and thus these methods provide a natural starting point for the analysis of spatio-temporal point process data. We restrict our attention to the spatio-temporal product density function......, and develop a non-parametric edge-corrected kernel estimate of the product density under the second-order intensity-reweighted stationary hypothesis. The expectation and variance of the estimator are obtained, and closed form expressions derived under the Poisson case. A detailed simulation study is presented...... to compare our close expression for the variance with estimated ones for Poisson cases. The simulation experiments show that the theoretical form for the variance gives acceptable values, which can be used in practice. Finally, we apply the resulting estimator to data on the spatio-temporal distribution...

Spatio-Temporal Rule Mining

DEFF Research Database (Denmark)

Gidofalvi, Gyozo; Pedersen, Torben Bach

2005-01-01

Recent advances in communication and information technology, such as the increasing accuracy of GPS technology and the miniaturization of wireless communication devices pave the road for Location-Based Services (LBS). To achieve high quality for such services, spatio-temporal data mining techniques...... are needed. In this paper, we describe experiences with spatio-temporal rule mining in a Danish data mining company. First, a number of real world spatio-temporal data sets are described, leading to a taxonomy of spatio-temporal data. Second, the paper describes a general methodology that transforms...... the spatio-temporal rule mining task to the traditional market basket analysis task and applies it to the described data sets, enabling traditional association rule mining methods to discover spatio-temporal rules for LBS. Finally, unique issues in spatio-temporal rule mining are identified and discussed....

Temporal stability of soil moisture under different land uses/cover in the Loess Plateau based on a finer spatiotemporal scale

OpenAIRE

Zhou, J.; Fu, B. J.; Lü, N.; Gao, G. Y.; Lü, Y. H.; Wang, S.

2013-01-01

The Temporal stability of soil moisture (TSSM) is an important factor to evaluate the value of available water resources in a water-controlled ecosystem. In this study we used the evapotranspiration-TSSM (ET-TSSM) model and a new sampling design to examine the soil water dynamics and water balance of different land uses/cover types in a hilly landscape of the Loess Plateau under a finer spatiotemporal scale. Our primary focus is to examine the difference amo...

Computational modeling of the behavior of nuclear materials (2). Molecular simulations for nuclear materials. Current situation and future perspective

International Nuclear Information System (INIS)

Okita, Taira; Itakura, Mitsuhiro

2017-01-01

Molecular simulations for nuclear materials aim to reproduce atomistic-scale phenomena induced by irradiation and infer the change in material properties. In the present work, recent progress in this field is presented. In particular, the following three topics are explained: (1) Quantification of lattice defects formation process induced by fast neutron collision. (2) Identification of dislocation-channeling mechanism induced by interactions between defect clusters and dislocations. (3) Modeling of the three dimensional movement of defect clusters using molecular dynamics and kinetic Monte Carlo simulations. (author)

Improving the Performance of the Extreme-scale Simulator

Energy Technology Data Exchange (ETDEWEB)

Engelmann, Christian [ORNL; Naughton III, Thomas J [ORNL

2014-01-01

Investigating the performance of parallel applications at scale on future high-performance computing (HPC) architectures and the performance impact of different architecture choices is an important component of HPC hardware/software co-design. The Extreme-scale Simulator (xSim) is a simulation-based toolkit for investigating the performance of parallel applications at scale. xSim scales to millions of simulated Message Passing Interface (MPI) processes. The overhead introduced by a simulation tool is an important performance and productivity aspect. This paper documents two improvements to xSim: (1) a new deadlock resolution protocol to reduce the parallel discrete event simulation management overhead and (2) a new simulated MPI message matching algorithm to reduce the oversubscription management overhead. The results clearly show a significant performance improvement, such as by reducing the simulation overhead for running the NAS Parallel Benchmark suite inside the simulator from 1,020\\% to 238% for the conjugate gradient (CG) benchmark and from 102% to 0% for the embarrassingly parallel (EP) and benchmark, as well as, from 37,511% to 13,808% for CG and from 3,332% to 204% for EP with accurate process failure simulation.

Dynamics of Surfactant Clustering at Interfaces and Its Influence on the Interfacial Tension: Atomistic Simulation of a Sodium Hexadecane-Benzene Sulfonate-Tetradecane-Water System.

Science.gov (United States)

Paredes, Ricardo; Fariñas-Sánchez, Ana Isabel; Medina-Rodrı Guez, Bryan; Samaniego, Samantha; Aray, Yosslen; Álvarez, Luis Javier

2018-03-06

The process of equilibration of the tetradecane-water interface in the presence of sodium hexadecane-benzene sulfonate is studied using intensive atomistic molecular dynamics simulations. Starting as an initial point with all of the surfactants at the interface, it is obtained that the equilibration time of the interface (several microseconds) is orders of magnitude higher than previously reported simulated times. There is strong evidence that this slow equilibration process is due to the aggregation of surfactants molecules on the interface. To determine this fact, temporal evolution of interfacial tension and interfacial formation energy are studied and their temporal variations are correlated with cluster formation. To study cluster evolution, the mean cluster size and the probability that a molecule of surfactant chosen at random is free are obtained as a function of time. Cluster size distribution is estimated, and it is observed that some of the molecules remain free, whereas the rest agglomerate. Additionally, the temporal evolution of the interfacial thickness and the structure of the surfactant molecules on the interface are studied. It is observed how this structure depends on whether the molecules agglomerate or not.

Thermodynamics of low-temperature phyllosilicates: from a macroscopic perspective towards achieving atomistic simulation

International Nuclear Information System (INIS)

Dubacq, B.

2008-12-01

suggest several improvements to these methods. We used atomistic simulation to calculate the mixing enthalpy along two solid solutions binaries of interest in low-temperature petrology. Results are in agreement with observations in natural systems and confirm the importance of hydration in clay minerals stability. (author)

3D atomistic studies of fatigue behaviour of edge crack (0 0 1) in bcc iron loaded in mode i and II

Czech Academy of Sciences Publication Activity Database

Machová, Anna; Pokluda, J.; Uhnáková, Alena; Hora, Petr

2014-01-01

Roč. 66, September (2014), s. 11-19 ISSN 0142-1123 R&D Projects: GA ČR(CZ) GAP108/10/0698 Institutional support: RVO:61388998 Keywords : fatigue crack growth * bcc iron * 3D atomistic simulations * molecular dynamics Subject RIV: JQ - Machines ; Tools Impact factor: 2.275, year: 2014 www.elsevier.com/locate/ijfatigue

Dynamic strain-induced transformation: An atomic scale investigation

International Nuclear Information System (INIS)

Zhang, H.; Pradeep, K.G.; Mandal, S.; Ponge, D.; Springer, H.; Raabe, D.

2015-01-01

Phase transformations provide the most versatile access to the design of complex nanostructured alloys in terms of grain size, morphology, local chemical constitution etc. Here we study a special case of deformation induced phase transformation. More specifically, we investigate the atomistic mechanisms associated with dynamic strain-induced transformation (DSIT) in a dual-phased multicomponent iron-based alloy at high temperatures. DSIT phenomena and the associated secondary phase nucleation were observed at atomic scale using atom probe tomography. The obtained local chemical composition was used for simulating the nucleation process which revealed that DSIT, occurring during load exertion, proceeds by a diffusion-controlled nucleation process

A Mixed Land Cover Spatio-temporal Data Model Based on Object-oriented and Snapshot

Directory of Open Access Journals (Sweden)

LI Yinchao

2016-07-01

Full Text Available Spatio-temporal data model (STDM is one of the hot topics in the domains of spatio-temporal database and data analysis. There is a common view that a universal STDM is always of high complexity due to the various situation of spatio-temporal data. In this article, a mixed STDM is proposed based on object-oriented and snapshot models for modelling and analyzing landcover change (LCC. This model uses the object-oriented STDM to describe the spatio-temporal processes of land cover patches and organize their spatial and attributive properties. In the meantime, it uses the snapshot STDM to present the spatio-temporal distribution of LCC on the whole via snapshot images. The two types of models are spatially and temporally combined into a mixed version. In addition to presenting the spatio-temporal events themselves, this model could express the transformation events between different classes of spatio-temporal objects. It can be used to create database for historical data of LCC, do spatio-temporal statistics, simulation and data mining with the data. In this article, the LCC data in Heilongjiang province is used for case study to validate spatio-temporal data management and analysis abilities of mixed STDM, including creating database, spatio-temporal query, global evolution analysis and patches spatio-temporal process expression.

An efficient Monte Carlo algorithm for the fast equilibration and atomistic simulation of alkanethiol self-assembled monolayers on a Au(111) substrate.

Science.gov (United States)

Alexiadis, Orestis; Daoulas, Kostas Ch; Mavrantzas, Vlasis G

2008-01-31

A new Monte Carlo algorithm is presented for the simulation of atomistically detailed alkanethiol self-assembled monolayers (R-SH) on a Au(111) surface. Built on a set of simpler but also more complex (sometimes nonphysical) moves, the new algorithm is capable of efficiently driving all alkanethiol molecules to the Au(111) surface, thereby leading to full surface coverage, irrespective of the initial setup of the system. This circumvents a significant limitation of previous methods in which the simulations typically started from optimally packed structures on the substrate close to thermal equilibrium. Further, by considering an extended ensemble of configurations each one of which corresponds to a different value of the sulfur-sulfur repulsive core potential, sigmass, and by allowing for configurations to swap between systems characterized by different sigmass values, the new algorithm can adequately simulate model R-SH/Au(111) systems for values of sigmass ranging from 4.25 A corresponding to the Hautman-Klein molecular model (J. Chem. Phys. 1989, 91, 4994; 1990, 93, 7483) to 4.97 A corresponding to the Siepmann-McDonald model (Langmuir 1993, 9, 2351), and practically any chain length. Detailed results are presented quantifying the efficiency and robustness of the new method. Representative simulation data for the dependence of the structural and conformational properties of the formed monolayer on the details of the employed molecular model are reported and discussed; an investigation of the variation of molecular organization and ordering on the Au(111) substrate for three CH3-(CH2)n-SH/Au(111) systems with n=9, 15, and 21 is also included.

AN ADAPTIVE ORGANIZATION METHOD OF GEOVIDEO DATA FOR SPATIO-TEMPORAL ASSOCIATION ANALYSIS

Directory of Open Access Journals (Sweden)

C. Wu

2015-07-01

Full Text Available Public security incidents have been increasingly challenging to address with their new features, including large-scale mobility, multi-stage dynamic evolution, spatio-temporal concurrency and uncertainty in the complex urban environment, which require spatio-temporal association analysis among multiple regional video data for global cognition. However, the existing video data organizational methods that view video as a property of the spatial object or position in space dissever the spatio-temporal relationship of scattered video shots captured from multiple video channels, limit the query functions on interactive retrieval between a camera and its video clips and hinder the comprehensive management of event-related scattered video shots. GeoVideo, which maps video frames onto a geographic space, is a new approach to represent the geographic world, promote security monitoring in a spatial perspective and provide a highly feasible solution to this problem. This paper analyzes the large-scale personnel mobility in public safety events and proposes a multi-level, event-related organization method with massive GeoVideo data by spatio-temporal trajectory. This paper designs a unified object identify(ID structure to implicitly store the spatio-temporal relationship of scattered video clips and support the distributed storage management of massive cases. Finally, the validity and feasibility of this method are demonstrated through suspect tracking experiments.

Inferring spatial memory and spatiotemporal scaling from GPS data: comparing red deer Cervus elaphus movements with simulation models.

Science.gov (United States)

Gautestad, Arild O; Loe, Leif E; Mysterud, Atle

2013-05-01

1. Increased inference regarding underlying behavioural mechanisms of animal movement can be achieved by comparing GPS data with statistical mechanical movement models such as random walk and Lévy walk with known underlying behaviour and statistical properties. 2. GPS data are typically collected with ≥ 1 h intervals not exactly tracking every mechanistic step along the movement path, so a statistical mechanical model approach rather than a mechanistic approach is appropriate. However, comparisons require a coherent framework involving both scaling and memory aspects of the underlying process. Thus, simulation models have recently been extended to include memory-guided returns to previously visited patches, that is, site fidelity. 3. We define four main classes of movement, differing in incorporation of memory and scaling (based on respective intervals of the statistical fractal dimension D and presence/absence of site fidelity). Using three statistical protocols to estimate D and site fidelity, we compare these main movement classes with patterns observed in GPS data from 52 females of red deer (Cervus elaphus). 4. The results show best compliance with a scale-free and memory-enhanced kind of space use; that is, a power law distribution of step lengths, a fractal distribution of the spatial scatter of fixes and site fidelity. 5. Our study thus demonstrates how inference regarding memory effects and a hierarchical pattern of space use can be derived from analysis of GPS data. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Atomistic Structure of Mineral Nano-aggregates from Simulated Compaction and Dewatering.

Science.gov (United States)

Ho, Tuan Anh; Greathouse, Jeffery A; Wang, Yifeng; Criscenti, Louise J

2017-11-10

The porosity of clay aggregates is an important property governing chemical reactions and fluid flow in low-permeability geologic formations and clay-based engineered barrier systems. Pore spaces in clays include interlayer and interparticle pores. Under compaction and dewatering, the size and geometry of such pore spaces may vary significantly (sub-nanometer to microns) depending on ambient physical and chemical conditions. Here we report a molecular dynamics simulation method to construct a complex and realistic clay-like nanoparticle aggregate with interparticle pores and grain boundaries. The model structure is then used to investigate the effect of dewatering and water content on micro-porosity of the aggregates. The results suggest that slow dewatering would create more compact aggregates compared to fast dewatering. Furthermore, the amount of water present in the aggregates strongly affects the particle-particle interactions and hence the aggregate structure. Detailed analyses of particle-particle and water-particle interactions provide a molecular-scale view of porosity and texture development of the aggregates. The simulation method developed here may also aid in modeling the synthesis of nanostructured materials through self-assembly of nanoparticles.

Elucidating the atomistic mechanisms underpinning plasticity in Li-Si nanostructures

Science.gov (United States)

Yan, Xin; Gouissem, Afif; Guduru, Pradeep R.; Sharma, Pradeep

2017-10-01

Amorphous lithium-silicon (a-Li-Si), especially in nanostructure form, is an attractive high-capacity anode material for next-generation Li-ion batteries. During cycles of charging and discharging, a-Li-Si undergoes substantive inelastic deformation and exhibits microcracking. The mechanical response to repeated lithiation-delithiation eventually results in the loss of electrical contact and consequent decrease of capacity, thus underscoring the importance of studying the plasticity of a-Li-Si nanostructures. In recent years, a variety of phenomenological continuum theories have been introduced that purport to model plasticity and the electro-chemo-mechanical behavior of a-Li-Si. Unfortunately, the micromechanisms and atomistic considerations underlying plasticity in Li-Si material are not yet fully understood and this impedes the development of physics-based constitutive models. Conventional molecular dynamics, although extensively used to study this material, is grossly inadequate to resolve this matter. As is well known, conventional molecular dynamics simulations can only address phenomena with characteristic time scales of (at most) a microsecond. Accordingly, in such simulations, the mechanical behavior is deduced under conditions of very high strain rates (usually, 108s-1 or even higher). This limitation severely impacts a realistic assessment of rate-dependent effects. In this work, we attempt to circumvent the time-scale bottleneck of conventional molecular dynamics and provide novel insights into the mechanisms underpinning plastic deformation of Li-Si nanostructures. We utilize an approach that allows imposition of slow strain rates and involves the employment of a new and recently developed potential energy surface sampling method—the so-called autonomous basin climbing—to identify the local minima in the potential energy surface. Combined with other techniques, such as nudged elastic band, kinetic Monte Carlo and transition state theory, we assess

Estimating repetitive spatiotemporal patterns from resting-state brain activity data.

Science.gov (United States)

Takeda, Yusuke; Hiroe, Nobuo; Yamashita, Okito; Sato, Masa-Aki

2016-06-01

Repetitive spatiotemporal patterns in spontaneous brain activities have been widely examined in non-human studies. These studies have reported that such patterns reflect past experiences embedded in neural circuits. In human magnetoencephalography (MEG) and electroencephalography (EEG) studies, however, spatiotemporal patterns in resting-state brain activities have not been extensively examined. This is because estimating spatiotemporal patterns from resting-state MEG/EEG data is difficult due to their unknown onsets. Here, we propose a method to estimate repetitive spatiotemporal patterns from resting-state brain activity data, including MEG/EEG. Without the information of onsets, the proposed method can estimate several spatiotemporal patterns, even if they are overlapping. We verified the performance of the method by detailed simulation tests. Furthermore, we examined whether the proposed method could estimate the visual evoked magnetic fields (VEFs) without using stimulus onset information. The proposed method successfully detected the stimulus onsets and estimated the VEFs, implying the applicability of this method to real MEG data. The proposed method was applied to resting-state functional magnetic resonance imaging (fMRI) data and MEG data. The results revealed informative spatiotemporal patterns representing consecutive brain activities that dynamically change with time. Using this method, it is possible to reveal discrete events spontaneously occurring in our brains, such as memory retrieval. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Pattern formation and control of spatiotemporal chaos in a reaction diffusion prey–predator system supplying additional food

International Nuclear Information System (INIS)

Ghorai, Santu; Poria, Swarup

2016-01-01

Spatiotemporal dynamics of a predator–prey system in presence of spatial diffusion is investigated in presence of additional food exists for predators. Conditions for stability of Hopf as well as Turing patterns in a spatial domain are determined by making use of the linear stability analysis. Impact of additional food is clear from these conditions. Numerical simulation results are presented in order to validate the analytical findings. Finally numerical simulations are carried out around the steady state under zero flux boundary conditions. With the help of numerical simulations, the different types of spatial patterns (including stationary spatial pattern, oscillatory pattern, and spatiotemporal chaos) are identified in this diffusive predator–prey system in presence of additional food, depending on the quantity, quality of the additional food and the spatial domain and other parameters of the model. The key observation is that spatiotemporal chaos can be controlled supplying suitable additional food to predator. These investigations may be useful to understand complex spatiotemporal dynamics of population dynamical models in presence of additional food.

Adhesive contact: from atomistic model to continuum model

International Nuclear Information System (INIS)

Fan Kang-Qi; Jia Jian-Yuan; Zhu Ying-Min; Zhang Xiu-Yan

2011-01-01

Two types of Lennard-Jones potential are widely used in modeling adhesive contacts. However, the relationships between the parameters of the two types of Lennard-Jones potential are not well defined. This paper employs a self-consistent method to derive the Lennard-Jones surface force law from the interatomic Lennard-Jones potential with emphasis on the relationships between the parameters. The effect of using correct parameters in the adhesion models is demonstrated in single sphere-flat contact via continuum models and an atomistic model. Furthermore, the adhesion hysteresis behaviour is investigated, and the S-shaped force-distance relation is revealed by the atomistic model. It shows that the adhesion hysteresis loop is generated by the jump-to-contact and jump-off-contact, which are illustrated by the S-shaped force-distance curve. (atomic and molecular physics)

Molecular dynamics simulation of edge dislocation piled at cuboidal precipitate in Ni-based superalloy

International Nuclear Information System (INIS)

Yashiro, Kisaragi; Naito, Masato; Tomita, Yoshihiro

2003-01-01

In order to clarify the fundamental mechanism of dislocations in the γ/γ' microstructure of Ni-based superalloy, three molecular dynamics simulations are conducted on the behavior of edge dislocations nucleated from a free surface and proceeding in the pure Ni matrix (γ) toward cuboidal Ni 3 Al precipitates (γ') under shear force. One involves dislocations near the apices of two precipitates adjoining each other with the distance of 0.04 μm, as large as the width of the γ channel in real superalloys. Others simulate dislocations piled at the precipitates as well, however, the scale of the microstructure is smaller than that in real superalloys by one order of magnitude, and one of them have precipitates with atomistically sharp edge. Dislocations are pinned at precipitates and bowed-out in the γ channel, then they begin to penetrate into the precipitate at the edge in both the real-scale and smaller microstructures when the precipitates have blunt edges. On the other hand, an edge dislocation splits into a superpartial in the γ' precipitate and a misfit screw dislocation bridging between two adjacent precipitates at the atomistically sharp edge of γ' precipitates. It is also observed that two superpartials glide in the precipitate as a superdislocation with anti-phase boundary (APB), of which the width is evaluated to be about 4 nm. (author)

An integrated data model to estimate spatiotemporal occupancy, abundance, and colonization dynamics

Science.gov (United States)

Williams, Perry J.; Hooten, Mevin B.; Womble, Jamie N.; Esslinger, George G.; Bower, Michael R.; Hefley, Trevor J.

2017-01-01

Ecological invasions and colonizations occur dynamically through space and time. Estimating the distribution and abundance of colonizing species is critical for efficient management or conservation. We describe a statistical framework for simultaneously estimating spatiotemporal occupancy and abundance dynamics of a colonizing species. Our method accounts for several issues that are common when modeling spatiotemporal ecological data including multiple levels of detection probability, multiple data sources, and computational limitations that occur when making fine-scale inference over a large spatiotemporal domain. We apply the model to estimate the colonization dynamics of sea otters (Enhydra lutris) in Glacier Bay, in southeastern Alaska.

Assessing global vegetation activity using spatio-temporal Bayesian modelling

Science.gov (United States)

Mulder, Vera L.; van Eck, Christel M.; Friedlingstein, Pierre; Regnier, Pierre A. G.

2016-04-01

This work demonstrates the potential of modelling vegetation activity using a hierarchical Bayesian spatio-temporal model. This approach allows modelling changes in vegetation and climate simultaneous in space and time. Changes of vegetation activity such as phenology are modelled as a dynamic process depending on climate variability in both space and time. Additionally, differences in observed vegetation status can be contributed to other abiotic ecosystem properties, e.g. soil and terrain properties. Although these properties do not change in time, they do change in space and may provide valuable information in addition to the climate dynamics. The spatio-temporal Bayesian models were calibrated at a regional scale because the local trends in space and time can be better captured by the model. The regional subsets were defined according to the SREX segmentation, as defined by the IPCC. Each region is considered being relatively homogeneous in terms of large-scale climate and biomes, still capturing small-scale (grid-cell level) variability. Modelling within these regions is hence expected to be less uncertain due to the absence of these large-scale patterns, compared to a global approach. This overall modelling approach allows the comparison of model behavior for the different regions and may provide insights on the main dynamic processes driving the interaction between vegetation and climate within different regions. The data employed in this study encompasses the global datasets for soil properties (SoilGrids), terrain properties (Global Relief Model based on SRTM DEM and ETOPO), monthly time series of satellite-derived vegetation indices (GIMMS NDVI3g) and climate variables (Princeton Meteorological Forcing Dataset). The findings proved the potential of a spatio-temporal Bayesian modelling approach for assessing vegetation dynamics, at a regional scale. The observed interrelationships of the employed data and the different spatial and temporal trends support

Atomistic Modeling of Ion Conduction through the Voltage-Sensing Domain of the Shaker K+ Ion Channel.

Science.gov (United States)

Wood, Mona L; Freites, J Alfredo; Tombola, Francesco; Tobias, Douglas J

2017-04-20

Voltage-sensing domains (VSDs) sense changes in the membrane electrostatic potential and, through conformational changes, regulate a specific function. The VSDs of wild-type voltage-dependent K + , Na + , and Ca 2+ channels do not conduct ions, but they can become ion-permeable through pathological mutations in the VSD. Relatively little is known about the underlying mechanisms of conduction through VSDs. The most detailed studies have been performed on Shaker K + channel variants in which ion conduction through the VSD is manifested in electrophysiology experiments as a voltage-dependent inward current, the so-called omega current, which appears when the VSDs are in their resting state conformation. Only monovalent cations appear to permeate the Shaker VSD via a pathway that is believed to be, at least in part, the same as that followed by the S4 basic side chains during voltage-dependent activation. We performed μs-time scale atomistic molecular dynamics simulations of a cation-conducting variant of the Shaker VSD under applied electric fields in an experimentally validated resting-state conformation, embedded in a lipid bilayer surrounded by solutions containing guanidinium chloride or potassium chloride. Our simulations provide insights into the Shaker VSD permeation pathway, the protein-ion interactions that control permeation kinetics, and the mechanism of voltage-dependent activation of voltage-gated ion channels.

Spatiotemporal Data Mining: A Computational Perspective

Directory of Open Access Journals (Sweden)

Shashi Shekhar

2015-10-01

Full Text Available Explosive growth in geospatial and temporal data as well as the emergence of new technologies emphasize the need for automated discovery of spatiotemporal knowledge. Spatiotemporal data mining studies the process of discovering interesting and previously unknown, but potentially useful patterns from large spatiotemporal databases. It has broad application domains including ecology and environmental management, public safety, transportation, earth science, epidemiology, and climatology. The complexity of spatiotemporal data and intrinsic relationships limits the usefulness of conventional data science techniques for extracting spatiotemporal patterns. In this survey, we review recent computational techniques and tools in spatiotemporal data mining, focusing on several major pattern families: spatiotemporal outlier, spatiotemporal coupling and tele-coupling, spatiotemporal prediction, spatiotemporal partitioning and summarization, spatiotemporal hotspots, and change detection. Compared with other surveys in the literature, this paper emphasizes the statistical foundations of spatiotemporal data mining and provides comprehensive coverage of computational approaches for various pattern families. ISPRS Int. J. Geo-Inf. 2015, 4 2307 We also list popular software tools for spatiotemporal data analysis. The survey concludes with a look at future research needs.

Atomic-scale nanoindentation: detection and identification of single glide events in three dimensions by force microscopy

International Nuclear Information System (INIS)

Egberts, P; Bennewitz, R

2011-01-01

Indentation experiments on the nanometre scale have been performed by means of atomic force microscopy in ultra-high vacuum on KBr(100) surfaces. The surfaces yield in the form of discrete surface displacements with a typical length scale of 1 A. These surface displacements are detected in both normal and lateral directions. Measurement of the lateral tip displacement requires a load-dependent calibration due to the load dependence of the effective lateral compliance. Correlation of the lateral and normal displacements for each glide event allow identification of the activated slip system. The results are discussed in terms of the resolved shear stress in indentation experiments and of typical results in atomistic simulations of nanometre-scale indentation.

Integrated simulation of continuous-scale and discrete-scale radiative transfer in metal foams

Science.gov (United States)

Xia, Xin-Lin; Li, Yang; Sun, Chuang; Ai, Qing; Tan, He-Ping

2018-06-01

A novel integrated simulation of radiative transfer in metal foams is presented. It integrates the continuous-scale simulation with the direct discrete-scale simulation in a single computational domain. It relies on the coupling of the real discrete-scale foam geometry with the equivalent continuous-scale medium through a specially defined scale-coupled zone. This zone holds continuous but nonhomogeneous volumetric radiative properties. The scale-coupled approach is compared to the traditional continuous-scale approach using volumetric radiative properties in the equivalent participating medium and to the direct discrete-scale approach employing the real 3D foam geometry obtained by computed tomography. All the analyses are based on geometrical optics. The Monte Carlo ray-tracing procedure is used for computations of the absorbed radiative fluxes and the apparent radiative behaviors of metal foams. The results obtained by the three approaches are in tenable agreement. The scale-coupled approach is fully validated in calculating the apparent radiative behaviors of metal foams composed of very absorbing to very reflective struts and that composed of very rough to very smooth struts. This new approach leads to a reduction in computational time by approximately one order of magnitude compared to the direct discrete-scale approach. Meanwhile, it can offer information on the local geometry-dependent feature and at the same time the equivalent feature in an integrated simulation. This new approach is promising to combine the advantages of the continuous-scale approach (rapid calculations) and direct discrete-scale approach (accurate prediction of local radiative quantities).

Regionalised spatiotemporal rainfall and temperature models for flood studies in the Basque Country, Spain

Directory of Open Access Journals (Sweden)

P. Cowpertwait

2013-02-01

Full Text Available A spatiotemporal point process model of rainfall is fitted to data taken from three homogeneous regions in the Basque Country, Spain. The model is the superposition of two spatiotemporal Neyman–Scott processes, in which rain cells are modelled as discs with radii that follow exponential distributions. In addition, the model includes a parameter for the radius of storm discs, so that rain only occurs when both a cell and a storm disc overlap a point. The model is fitted to data for each month, taken from each of the three homogeneous regions, using a modified method of moments procedure that ensures a smooth seasonal variation in the parameter estimates.

Daily temperature data from 23 sites are used to fit a stochastic temperature model. A principal component analysis of the maximum daily temperatures across the sites indicates that 92% of the variance is explained by the first component, implying that this component can be used to account for spatial variation. A harmonic equation with autoregressive error terms is fitted to the first principal component. The temperature model is obtained by regressing the maximum daily temperature on the first principal component, an indicator variable for the region, and altitude. This, together with scaling and a regression model of temperature range, enables hourly temperatures to be predicted. Rainfall is included as an explanatory variable but has only a marginal influence when predicting temperatures.

A distributed model (TETIS; Francés et al., 2007 is calibrated for a selected catchment. Five hundred years of data are simulated using the rainfall and temperature models and used as input to the calibrated TETIS model to obtain simulated discharges to compare with observed discharges. Kolmogorov–Smirnov tests indicate that there is no significant difference in the distributions of observed and simulated maximum flows at the same sites, thus supporting the use of the spatiotemporal

Atomistic studies of nucleation of He clusters and bubbles in bcc iron

International Nuclear Information System (INIS)

Yang, L.; Deng, H.Q.; Gao, F.; Heinisch, H.L.; Kurtz, R.J.; Hu, S.Y.; Li, Y.L.; Zu, X.T.

2013-01-01

Atomistic simulations of the nucleation of He clusters and bubbles in bcc iron at 800 K have been carried out using the newly developed Fe–Fe interatomic potential, along with Ackland potential for the Fe–Fe interactions. Microstructure changes were analyzed in detail. We found that a He cluster with four He atoms is able to push out an iron interstitial from the cluster, creating a Frenkel pair. Small He clusters and self-interstitial atom (SIA) can migrate in the matrix, but He-vacancy (He-V) clusters are immobile. Most SIAs form clusters, and only the dislocation loops with a Burgers vector of b = 1/2 appear in the simulations. SIA clusters (or loops) are attached to He-V clusters for He implantation up to 1372 appm, while the He-V cluster–loop complexes with more than one He-V cluster are formed at the He concentration of 2057 appm and larger

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

Science.gov (United States)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

DEFF Research Database (Denmark)

Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

2008-01-01

. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

Dynamic characterizers of spatiotemporal intermittency

OpenAIRE

Gupte, Neelima; Jabeen, Zahera

2006-01-01

Systems of coupled sine circle maps show regimes of spatiotemporally intermittent behaviour with associated scaling exponents which belong to the DP class, as well as regimes of spatially intermittent behaviour (with associated regular dynamical behaviour) which do not belong to the DP class. Both types of behaviour are seen along the bifurcation boundaries of the synchronized solutions, and contribute distinct signatures to the dynamical characterizers of the system, viz. the distribution of...

Large-scale numerical simulations of plasmas

International Nuclear Information System (INIS)

Hamaguchi, Satoshi

2004-01-01

The recent trend of large scales simulations of fusion plasma and processing plasmas is briefly summarized. Many advanced simulation techniques have been developed for fusion plasmas and some of these techniques are now applied to analyses of processing plasmas. (author)

Atomistic studies of cation transport in tetragonal ZrO2 during zirconium corrosion

International Nuclear Information System (INIS)

Bai, Xian-Ming; Zhang, Yongfeng; Tonks, Michael R.

2015-01-01

Zirconium alloys are the major fuel cladding materials in current reactors. The water-side corrosion is a significant degradation mechanism of these alloys. During corrosion, the transport of oxidizing species in zirconium dioxide (ZrO 2 ) determines the corrosion kinetics. Previously, it has been argued that the outward diffusion of cations is important for forming protective oxides. In this work, the migration of Zr defects in tetragonal ZrO 2 is studied with temperature accelerated dynamics and molecular dynamics simulations. The results show that Zr interstitials have anisotropic diffusion and migrate preferentially along the [001] or c direction in tetragonal ZrO 2 . The compressive stresses can increase the Zr interstitial migration barrier significantly. The migration of Zr interstitials at a grain boundary is much slower than in a bulk oxide. The implications of these atomistic simulation results in the Zr corrosion are discussed. (authors)

Large-scale simulations with distributed computing: Asymptotic scaling of ballistic deposition

International Nuclear Information System (INIS)

Farnudi, Bahman; Vvedensky, Dimitri D

2011-01-01

Extensive kinetic Monte Carlo simulations are reported for ballistic deposition (BD) in (1 + 1) dimensions. The large system sizes L observed for the onset of asymptotic scaling (L ≅ 2 12 ) explains the widespread discrepancies in previous reports for exponents of BD in one and likely in higher dimensions. The exponents obtained directly from our simulations, α = 0.499 ± 0.004 and β = 0.336 ± 0.004, capture the exact values α = 1/2 and β = 1/3 for the one-dimensional Kardar-Parisi-Zhang equation. An analysis of our simulations suggests a criterion for identifying the onset of true asymptotic scaling, which enables a more informed evaluation of exponents for BD in higher dimensions. These simulations were made possible by the Simulation through Social Networking project at the Institute for Advanced Studies in Basic Sciences in 2007, which was re-launched in November 2010.

A universal preconditioner for simulating condensed phase materials

Energy Technology Data Exchange (ETDEWEB)

Packwood, David; Ortner, Christoph, E-mail: c.ortner@warwick.ac.uk [Mathematics Institute, University of Warwick, Coventry CV4 7AL (United Kingdom); Kermode, James, E-mail: j.r.kermode@warwick.ac.uk [Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL (United Kingdom); Mones, Letif [Mathematics Institute, University of Warwick, Coventry CV4 7AL (United Kingdom); Engineering Laboratory, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ (United Kingdom); Bernstein, Noam [Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC 20375 (United States); Woolley, John [Department of Physics, University of Warwick, Coventry CV4 7AL (United Kingdom); Gould, Nicholas [Scientific Computing Department, STFC-Rutherford Appleton Laboratory Chilton, Oxfordshire OX11 0QX (United Kingdom); Csányi, Gábor, E-mail: gc121@cam.ac.uk [Engineering Laboratory, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ (United Kingdom)

2016-04-28

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

Atomistic modeling of ion beam induced amorphization in silicon

International Nuclear Information System (INIS)

Pelaz, Lourdes; Marques, Luis A.; Lopez, Pedro; Santos, Ivan; Aboy, Maria; Barbolla, Juan

2005-01-01

Ion beam induced amorphization in Si has attracted significant interest since the beginning of the use of ion implantation for the fabrication of Si devices. Nowadays, a renewed interest in the modeling of amorphization mechanisms at atomic level has arisen due to the use of preamorphizing implants and high dopant implantation doses for the fabrication of nanometric-scale Si devices. In this work, we briefly describe the existing phenomenological and defect-based amorphization models. We focus on the atomistic model we have developed to describe ion beam induced amorphization in Si. In our model, the building block for the amorphous phase is the bond defect or IV pair, whose stability increases with the number of surrounding IV pairs. This feature explains the regrowth behavior of different damage topologies and the kinetics of the crystalline to amorphous transition. The model provides excellent quantitative agreement with experimental results

Spatio-temporal diffusion of dynamic PET images

International Nuclear Information System (INIS)

Tauber, C; Chalon, S; Guilloteau, D; Stute, S; Buvat, I; Chau, M; Spiteri, P

2011-01-01

Positron emission tomography (PET) images are corrupted by noise. This is especially true in dynamic PET imaging where short frames are required to capture the peak of activity concentration after the radiotracer injection. High noise results in a possible bias in quantification, as the compartmental models used to estimate the kinetic parameters are sensitive to noise. This paper describes a new post-reconstruction filter to increase the signal-to-noise ratio in dynamic PET imaging. It consists in a spatio-temporal robust diffusion of the 4D image based on the time activity curve (TAC) in each voxel. It reduces the noise in homogeneous areas while preserving the distinct kinetics in regions of interest corresponding to different underlying physiological processes. Neither anatomical priors nor the kinetic model are required. We propose an automatic selection of the scale parameter involved in the diffusion process based on a robust statistical analysis of the distances between TACs. The method is evaluated using Monte Carlo simulations of brain activity distributions. We demonstrate the usefulness of the method and its superior performance over two other post-reconstruction spatial and temporal filters. Our simulations suggest that the proposed method can be used to significantly increase the signal-to-noise ratio in dynamic PET imaging.

Learning from large scale neural simulations

DEFF Research Database (Denmark)

Serban, Maria

2017-01-01

Large-scale neural simulations have the marks of a distinct methodology which can be fruitfully deployed to advance scientific understanding of the human brain. Computer simulation studies can be used to produce surrogate observational data for better conceptual models and new how...

Simulating the production of free defects in irradiated metals

International Nuclear Information System (INIS)

Heinisch, H.L.

1995-01-01

Under cascade-producing irradiation by high energy neutrons or charged particles, only a small fraction of the initially displaced atoms contribute to the population of free defects that are available to migrate throughout the metal and cause microstructural changes. Although, in principle, computer simulations of free defect production could best be done using molecular dynamics, in practice, the wide ranges of time and distance scales involved can be done only by a combination of atomistic models that employ various levels of approximation. An atomic-scale, multi-model approach has been developed that combines molecular dynamics, binary collision models and stochastic annealing simulation. The annealing simulation is utilized in calibrating binary collision simulations to the results of molecular dynamics calculations, as well as to model the subsequent migration of the defects on more macroscopic time and size scales. The annealing simulation and the method of calibrating the multi-model approach are discussed, and the results of simulations of cascades in copper are presented. The temperature dependence of free defect production following simulated annealing of isolated cascades in copper shows a differential in the fractions of free vacancies and interstitial defects escaping from the cascade above stage V. This differential, a consequence of the direct formation of interstitial clusters in cascades and the relative thermal stability of vacancy and interstitial clusters during subsequent annealing, is the basis for the production bias mechanism of void swelling. (orig.)

Spatiotemporal dynamics of a digital phase-locked loop based coupled map lattice system

Energy Technology Data Exchange (ETDEWEB)

Banerjee, Tanmoy, E-mail: tbanerjee@phys.buruniv.ac.in; Paul, Bishwajit; Sarkar, B. C. [Department of Physics, University of Burdwan, Burdwan, West Bengal 713 104 (India)

2014-03-15

We explore the spatiotemporal dynamics of a coupled map lattice (CML) system, which is realized with a one dimensional array of locally coupled digital phase-locked loops (DPLLs). DPLL is a nonlinear feedback-controlled system widely used as an important building block of electronic communication systems. We derive the phase-error equation of the spatially extended system of coupled DPLLs, which resembles a form of the equation of a CML system. We carry out stability analysis for the synchronized homogeneous solutions using the circulant matrix formalism. It is shown through extensive numerical simulations that with the variation of nonlinearity parameter and coupling strength the system shows transitions among several generic features of spatiotemporal dynamics, viz., synchronized fixed point solution, frozen random pattern, pattern selection, spatiotemporal intermittency, and fully developed spatiotemporal chaos. We quantify the spatiotemporal dynamics using quantitative measures like average quadratic deviation and spatial correlation function. We emphasize that instead of using an idealized model of CML, which is usually employed to observe the spatiotemporal behaviors, we consider a real world physical system and establish the existence of spatiotemporal chaos and other patterns in this system. We also discuss the importance of the present study in engineering application like removal of clock-skew in parallel processors.

Spatiotemporal radiotherapy planning using a global optimization approach

Science.gov (United States)

Adibi, Ali; Salari, Ehsan

2018-02-01

This paper aims at quantifying the extent of potential therapeutic gain, measured using biologically effective dose (BED), that can be achieved by altering the radiation dose distribution over treatment sessions in fractionated radiotherapy. To that end, a spatiotemporally integrated planning approach is developed, where the spatial and temporal dose modulations are optimized simultaneously. The concept of equivalent uniform BED (EUBED) is used to quantify and compare the clinical quality of spatiotemporally heterogeneous dose distributions in target and critical structures. This gives rise to a large-scale non-convex treatment-plan optimization problem, which is solved using global optimization techniques. The proposed spatiotemporal planning approach is tested on two stylized cancer cases resembling two different tumor sites and sensitivity analysis is performed for radio-biological and EUBED parameters. Numerical results validate that spatiotemporal plans are capable of delivering a larger BED to the target volume without increasing the BED in critical structures compared to conventional time-invariant plans. In particular, this additional gain is attributed to the irradiation of different regions of the target volume at different treatment sessions. Additionally, the trade-off between the potential therapeutic gain and the number of distinct dose distributions is quantified, which suggests a diminishing marginal gain as the number of dose distributions increases.

Modelling of radiation induced segregation in austenitic Fe alloys at the atomistic level

International Nuclear Information System (INIS)

Piochaud, Jean-Baptiste

2013-01-01

In pressurized water reactors, under irradiation internal structures are subject of irradiation assisted stress corrosion cracking which is influenced by radiation induced segregation (RIS). In this work RIS of 316 stainless steels is modelled considering a model ternary Fe-10Ni-20Cr alloy. For this purpose we have built an Fe-Ni-Cr pair interaction model to simulate RIS at the atomistic level using an atomistic kinetic Monte Carlo approach. The pair interactions have been deduced from density functional theory (DFT) data available in the pure fcc systems but also from DFT calculations we have performed in the Fe-10Ni-20Cr target alloy. Point defect formation energies were calculated and found to depend strongly on the local environment of the defect. As a consequence, a rather good estimation of these energies can be obtained from the knowledge of the number and respective positions of the Ni and Cr atoms in the vicinity of the defect. This work shows that a model based only on interaction parameters between elements positioned in perfect lattice sites (solute atoms and vacancy) cannot capture alone both the thermodynamic and the kinetic aspect of RIS. A more accurate of estimating the barriers encountered by the diffusing species is required than the one used in our model, which has to depend on the saddle point environment. This study therefore shows thus the need to estimate point defect migration energies using the DFT approach to calibrate a model that can be used in the framework of atomic kinetic Monte Carlo simulations. We also found that the reproduction by our pair interaction model of DFT data for the self-interstitial atoms was found to be incompatible with the modelling of RIS under electron irradiation. (author)

GISpark: A Geospatial Distributed Computing Platform for Spatiotemporal Big Data

Science.gov (United States)

Wang, S.; Zhong, E.; Wang, E.; Zhong, Y.; Cai, W.; Li, S.; Gao, S.

2016-12-01

Geospatial data are growing exponentially because of the proliferation of cost effective and ubiquitous positioning technologies such as global remote-sensing satellites and location-based devices. Analyzing large amounts of geospatial data can provide great value for both industrial and scientific applications. Data- and compute- intensive characteristics inherent in geospatial big data increasingly pose great challenges to technologies of data storing, computing and analyzing. Such challenges require a scalable and efficient architecture that can store, query, analyze, and visualize large-scale spatiotemporal data. Therefore, we developed GISpark - a geospatial distributed computing platform for processing large-scale vector, raster and stream data. GISpark is constructed based on the latest virtualized computing infrastructures and distributed computing architecture. OpenStack and Docker are used to build multi-user hosting cloud computing infrastructure for GISpark. The virtual storage systems such as HDFS, Ceph, MongoDB are combined and adopted for spatiotemporal data storage management. Spark-based algorithm framework is developed for efficient parallel computing. Within this framework, SuperMap GIScript and various open-source GIS libraries can be integrated into GISpark. GISpark can also integrated with scientific computing environment (e.g., Anaconda), interactive computing web applications (e.g., Jupyter notebook), and machine learning tools (e.g., TensorFlow/Orange). The associated geospatial facilities of GISpark in conjunction with the scientific computing environment, exploratory spatial data analysis tools, temporal data management and analysis systems make up a powerful geospatial computing tool. GISpark not only provides spatiotemporal big data processing capacity in the geospatial field, but also provides spatiotemporal computational model and advanced geospatial visualization tools that deals with other domains related with spatial property. We

Atomistic simulation of nanoformed metallic glass

Energy Technology Data Exchange (ETDEWEB)

Wu, Cheng-Da, E-mail: nanowu@cycu.edu.tw

2015-07-15

Highlights: • STZ forms at substrate surface underneath punch. • Atoms underneath punch have higher speeds at larger mold displacement. • Stick-slip phenomenon becomes more obvious with increasing imprint speed. • Great pattern transfer is obtained with unloading at low temperatures. - Abstract: The effects of forming speed and temperature on the forming mechanism and mechanics of Cu{sub 50}Zr{sub 25}Ti{sub 25} metallic glass are studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. These effects are investigated in terms of atomic trajectories, flow field, slip vectors, internal energy, radial distribution function, and elastic recovery of nanoimprint lithography (NIL) patterns. The simulation results show that a shear transformation zone (STZ) forms at the substrate surface underneath the mold during the forming process. The STZ area increases with mold displacement (D). The movement speed of substrate atoms underneath the mold increases with increasing D value. The movement directions of substrate atoms underneath the mold are more agreeable for a larger D value. The stick-slip phenomenon becomes more obvious with increasing D value and imprint speed. The substrate energy increases with increasing imprint speed and temperature. Great NIL pattern transfer is obtained with unloading at low temperatures (e.g., room temperature)

Adjusted functional boxplots for spatio-temporal data visualization and outlier detection

KAUST Repository

Sun, Ying; Genton, Marc G.

2011-01-01

This article proposes a simulation-based method to adjust functional boxplots for correlations when visualizing functional and spatio-temporal data, as well as detecting outliers. We start by investigating the relationship between the spatio

Spatiotemporal Thinking in the Geosciences

Science.gov (United States)

Shipley, T. F.; Manduca, C. A.; Ormand, C. J.; Tikoff, B.

2011-12-01

Reasoning about spatial relations is a critical skill for geoscientists. Within the geosciences different disciplines may reason about different sorts of relationships. These relationships may span vastly different spatial and temporal scales (from the spatial alignment in atoms in crystals to the changes in the shape of plates). As part of work in a research center on spatial thinking in STEM education, we have been working to classify the spatial skills required in geology, develop tests for each spatial skill, and develop the cognitive science tools to promote the critical spatial reasoning skills. Research in psychology, neurology and linguistics supports a broad classification of spatial skills along two dimensions: one versus many objects (which roughly translates to object- focused and navigation focused skills) and static versus dynamic spatial relations. The talk will focus on the interaction of space and time in spatial cognition in the geosciences. We are working to develop measures of skill in visualizing spatiotemporal changes. A new test developed to measure visualization of brittle deformations will be presented. This is a skill that has not been clearly recognized in the cognitive science research domain and thus illustrates the value of interdisciplinary work that combines geosciences with cognitive sciences. Teaching spatiotemporal concepts can be challenging. Recent theoretical work suggests analogical reasoning can be a powerful tool to aid student learning to reason about temporal relations using spatial skills. Recent work in our lab has found that progressive alignment of spatial and temporal scales promotes accurate reasoning about temporal relations at geological time scales.

Simulations of atomic-scale sliding friction

DEFF Research Database (Denmark)

Sørensen, Mads Reinholdt; Jacobsen, Karsten Wedel; Stoltze, Per

1996-01-01

Simulation studies of atomic-scale sliding friction have been performed for a number of tip-surface and surface-surface contacts consisting of copper atoms. Both geometrically very simple tip-surface structures and more realistic interface necks formed by simulated annealing have been studied....... Kinetic friction is observed to be caused by atomic-scale Stick and slip which occurs by nucleation and subsequent motion of dislocations preferably between close-packed {111} planes. Stick and slip seems ro occur in different situations. For single crystalline contacts without grain boundaries...... pinning of atoms near the boundary of the interface and is therefore more easily observed for smaller contacts. Depending on crystal orientation and load, frictional wear can also be seen in the simulations. In particular, for the annealed interface-necks which model contacts created by scanning tunneling...

An Overview of the State of the Art in Atomistic and Multiscale Simulation of Fracture

Science.gov (United States)

Saether, Erik; Yamakov, Vesselin; Phillips, Dawn R.; Glaessgen, Edward H.

2009-01-01

The emerging field of nanomechanics is providing a new focus in the study of the mechanics of materials, particularly in simulating fundamental atomic mechanisms involved in the initiation and evolution of damage. Simulating fundamental material processes using first principles in physics strongly motivates the formulation of computational multiscale methods to link macroscopic failure to the underlying atomic processes from which all material behavior originates. This report gives an overview of the state of the art in applying concurrent and sequential multiscale methods to analyze damage and failure mechanisms across length scales.

Final Report for DE-FG02-99ER45795

Energy Technology Data Exchange (ETDEWEB)

Wilkins, John Warren [The Ohio State Univ., Columbus, OH (United States)

2015-12-31

The research supported by this grant focuses on atomistic studies of defects, phase transitions, electronic and magnetic properties, and mechanical behaviors of materials. We have been studying novel properties of various emerging nanoscale materials on multiple levels of length and time scales, and have made accurate predictions on many technologically important properties. A significant part of our research has been devoted to exploring properties of novel nano-scale materials by pushing the limit of quantum mechanical simulations, and development of a rigorous scheme to design accurate classical inter-atomic potentials for larger scale atomistic simulations for many technologically important metals and metal alloys.

Spatio-Temporal Super-Resolution Reconstruction of Remote-Sensing Images Based on Adaptive Multi-Scale Detail Enhancement.

Science.gov (United States)

Zhu, Hong; Tang, Xinming; Xie, Junfeng; Song, Weidong; Mo, Fan; Gao, Xiaoming

2018-02-07

There are many problems in existing reconstruction-based super-resolution algorithms, such as the lack of texture-feature representation and of high-frequency details. Multi-scale detail enhancement can produce more texture information and high-frequency information. Therefore, super-resolution reconstruction of remote-sensing images based on adaptive multi-scale detail enhancement (AMDE-SR) is proposed in this paper. First, the information entropy of each remote-sensing image is calculated, and the image with the maximum entropy value is regarded as the reference image. Subsequently, spatio-temporal remote-sensing images are processed using phase normalization, which is to reduce the time phase difference of image data and enhance the complementarity of information. The multi-scale image information is then decomposed using the L ₀ gradient minimization model, and the non-redundant information is processed by difference calculation and expanding non-redundant layers and the redundant layer by the iterative back-projection (IBP) technique. The different-scale non-redundant information is adaptive-weighted and fused using cross-entropy. Finally, a nonlinear texture-detail-enhancement function is built to improve the scope of small details, and the peak signal-to-noise ratio (PSNR) is used as an iterative constraint. Ultimately, high-resolution remote-sensing images with abundant texture information are obtained by iterative optimization. Real results show an average gain in entropy of up to 0.42 dB for an up-scaling of 2 and a significant promotion gain in enhancement measure evaluation for an up-scaling of 2. The experimental results show that the performance of the AMED-SR method is better than existing super-resolution reconstruction methods in terms of visual and accuracy improvements.

Spatio-Temporal Super-Resolution Reconstruction of Remote-Sensing Images Based on Adaptive Multi-Scale Detail Enhancement

Science.gov (United States)

Zhu, Hong; Tang, Xinming; Xie, Junfeng; Song, Weidong; Mo, Fan; Gao, Xiaoming

2018-01-01

There are many problems in existing reconstruction-based super-resolution algorithms, such as the lack of texture-feature representation and of high-frequency details. Multi-scale detail enhancement can produce more texture information and high-frequency information. Therefore, super-resolution reconstruction of remote-sensing images based on adaptive multi-scale detail enhancement (AMDE-SR) is proposed in this paper. First, the information entropy of each remote-sensing image is calculated, and the image with the maximum entropy value is regarded as the reference image. Subsequently, spatio-temporal remote-sensing images are processed using phase normalization, which is to reduce the time phase difference of image data and enhance the complementarity of information. The multi-scale image information is then decomposed using the L0 gradient minimization model, and the non-redundant information is processed by difference calculation and expanding non-redundant layers and the redundant layer by the iterative back-projection (IBP) technique. The different-scale non-redundant information is adaptive-weighted and fused using cross-entropy. Finally, a nonlinear texture-detail-enhancement function is built to improve the scope of small details, and the peak signal-to-noise ratio (PSNR) is used as an iterative constraint. Ultimately, high-resolution remote-sensing images with abundant texture information are obtained by iterative optimization. Real results show an average gain in entropy of up to 0.42 dB for an up-scaling of 2 and a significant promotion gain in enhancement measure evaluation for an up-scaling of 2. The experimental results show that the performance of the AMED-SR method is better than existing super-resolution reconstruction methods in terms of visual and accuracy improvements. PMID:29414893

Tunable thermodynamic stability of Au-CuPt core-shell trimetallic nanoparticles by controlling the alloy composition: insights from atomistic simulations.

Science.gov (United States)

Huang, Rao; Shao, Gui-Fang; Wen, Yu-Hua; Sun, Shi-Gang

2014-11-07

A microscopic understanding of the thermal stability of metallic core-shell nanoparticles is of importance for their synthesis and ultimately application in catalysis. In this article, molecular dynamics simulations have been employed to investigate the thermodynamic evolution of Au-CuPt core-shell trimetallic nanoparticles with various Cu/Pt ratios during heating processes. Our results show that the thermodynamic stability of these nanoparticles is remarkably enhanced upon rising Pt compositions in the CuPt shell. The melting of all the nanoparticles initiates at surface and gradually spreads into the core. Due to the lattice mismatch among Au, Cu and Pt, stacking faults have been observed in the shell and their numbers are associated with the Cu/Pt ratios. With the increasing temperature, they have reduced continuously for the Cu-dominated shell while more stacking faults have been produced for the Pt-dominated shell because of the significantly different thermal expansion coefficients of the three metals. Beyond the overall melting, all nanoparticles transform into a trimetallic mixing alloy coated by an Au-dominated surface. This work provides a fundamental perspective on the thermodynamic behaviors of trimetallic, even multimetallic, nanoparticles at the atomistic level, indicating that controlling the alloy composition is an effective strategy to realize tunable thermal stability of metallic nanocatalysts.

Multi-scale simulation for homogenization of cement media

International Nuclear Information System (INIS)

Abballe, T.

2011-01-01

To solve diffusion problems on cement media, two scales must be taken into account: a fine scale, which describes the micrometers wide microstructures present in the media, and a work scale, which is usually a few meters long. Direct numerical simulations are almost impossible because of the huge computational resources (memory, CPU time) required to assess both scales at the same time. To overcome this problem, we present in this thesis multi-scale resolution methods using both Finite Volumes and Finite Elements, along with their efficient implementations. More precisely, we developed a multi-scale simulation tool which uses the SALOME platform to mesh domains and post-process data, and the parallel calculation code MPCube to solve problems. This SALOME/MPCube tool can solve automatically and efficiently multi-scale simulations. Parallel structure of computer clusters can be use to dispatch the more time-consuming tasks. We optimized most functions to account for cement media specificities. We presents numerical experiments on various cement media samples, e.g. mortar and cement paste. From these results, we manage to compute a numerical effective diffusivity of our cement media and to reconstruct a fine scale solution. (author) [fr

Spatiotemporal models of global soil organic carbon stock to support land degradation assessments at regional and global scales: limitations, challenges and opportunities

Science.gov (United States)

Hengl, Tomislav; Heuvelink, Gerard; Sanderman, Jonathan; MacMillan, Robert

2017-04-01

There is an increasing interest in fitting and applying spatiotemporal models that can be used to assess and monitor soil organic carbon stocks (SOCS), for example, in support of the '4 pourmille' initiative aiming at soil carbon sequestration towards climate change adaptation and mitigation and UN's Land Degradation Neutrality indicators and similar degradation assessment projects at regional and global scales. The land cover mapping community has already produced several spatiotemporal data sets with global coverage and at relatively fine resolution e.g. USGS MODIS land cover annual maps for period 2000-2014; European Space Agency land cover maps at 300 m resolution for the year 2000, 2005 and 2010; Chinese GlobeLand30 dataset available for years 2000 and 2010; Columbia University's WRI GlobalForestWatch with deforestation maps at 30 m resolution for the period 2000-2016 (Hansen et al. 2013). These data sets can be used for land degradation assessment and scenario testing at global and regional scales (Wei et al 2014). Currently, however, no compatible global spatiotemporal data sets exist on status of soil quality and/or soil health (Powlson et al. 2013). This paper describes an initial effort to devise and evaluate a procedure for mapping spatio-temporal changes in SOC stocks using a complete stack of soil forming factors (climate, relief, land cover, land use, lithology and living organisms) represented mainly through remote sensing based time series of Earth images. For model building we used some 75,000 geo-referenced soil profiles and a stacks space-time covariates (land cover, land use, biomass, climate) at two standard resolutions: (1) 10 km resolution with data available for period 1920-2014 and (2) 1000 m resolution with data available for period 2000-2014. The initial results show that, although it is technically feasible to produce space time estimates of SOCS that demonstrate the procedure, the estimates are relatively uncertain (<45% of variation

Precipitation-productivity Relation in Grassland in Northern China: Investigations at Multiple Spatiotemporal Scales

Science.gov (United States)

Hu, Z.

2017-12-01

Climate change is predicted to cause dramatic variability in precipitation regime, not only in terms of change in annual precipitation amount, but also in precipitation seasonal distribution and precipitation event characteristics (high frenquency extrem precipitation, larger but fewer precipitation events), which combined to influence productivity of grassland in arid and semiarid regions. In this study, combining remote sensing products with in-situ measurements of aboveground net primary productivity (ANPP) and gross primary productivity (GPP) data from eddy covariance system in grassland of northern China, we quantified the effects of spatio-temporal vairation in precipitation on productivity from local sites to region scale. We found that, for an individual precipitation event, the duration of GPP-response to the individual precipitation event and the maximum absolute GPP response induced by the individual precipitation event increased linearly with the size of precipitation events. Comparison of the productivity-precipitation relationships between multi-sites determined that the predominant characteristics of precipitation events (PEC) that affected GPP differed remarkably between the water-limited temperate steppe and the temperature-limited alpine meadow. The number of heavy precipitation events (>10 mm d-1) was the most important PEC to impact GPP in the temperate steppe through affecting soil moisture at different soil profiles, while precipitation interval was the factor that affected GPP most in the alpine meadow via its effects on temperature. At the region scale, shape of ANPP-precipitation relationship varies with distinct spatial scales, and besides annual precipitation, precipitation seasonal distribution also has comparable impacts on spatial variation in ANPP. Temporal variability in ANPP was lower at both the dry and wet end, and peaked at a precipitation of 243.1±3.5mm, which is the transition region between typical steppe and desert steppe

Probabilistic Simulation of Multi-Scale Composite Behavior

Science.gov (United States)

Chamis, Christos C.

2012-01-01

A methodology is developed to computationally assess the non-deterministic composite response at all composite scales (from micro to structural) due to the uncertainties in the constituent (fiber and matrix) properties, in the fabrication process and in structural variables (primitive variables). The methodology is computationally efficient for simulating the probability distributions of composite behavior, such as material properties, laminate and structural responses. Bi-products of the methodology are probabilistic sensitivities of the composite primitive variables. The methodology has been implemented into the computer codes PICAN (Probabilistic Integrated Composite ANalyzer) and IPACS (Integrated Probabilistic Assessment of Composite Structures). The accuracy and efficiency of this methodology are demonstrated by simulating the uncertainties in composite typical laminates and comparing the results with the Monte Carlo simulation method. Available experimental data of composite laminate behavior at all scales fall within the scatters predicted by PICAN. Multi-scaling is extended to simulate probabilistic thermo-mechanical fatigue and to simulate the probabilistic design of a composite redome in order to illustrate its versatility. Results show that probabilistic fatigue can be simulated for different temperature amplitudes and for different cyclic stress magnitudes. Results also show that laminate configurations can be selected to increase the redome reliability by several orders of magnitude without increasing the laminate thickness--a unique feature of structural composites. The old reference denotes that nothing fundamental has been done since that time.

A multi-scale modeling of surface effect via the modified boundary Cauchy-Born model

Energy Technology Data Exchange (ETDEWEB)

Khoei, A.R., E-mail: arkhoei@sharif.edu; Aramoon, A.

2012-10-01

In this paper, a new multi-scale approach is presented based on the modified boundary Cauchy-Born (MBCB) technique to model the surface effects of nano-structures. The salient point of the MBCB model is the definition of radial quadrature used in the surface elements which is an indicator of material behavior. The characteristics of quadrature are derived by interpolating data from atoms laid in a circular support around the quadrature, in a least-square scene. The total-Lagrangian formulation is derived for the equivalent continua by employing the Cauchy-Born hypothesis for calculating the strain energy density function of the continua. The numerical results of the proposed method are compared with direct atomistic and finite element simulation results to indicate that the proposed technique provides promising results for modeling surface effects of nano-structures. - Highlights: Black-Right-Pointing-Pointer A multi-scale approach is presented to model the surface effects in nano-structures. Black-Right-Pointing-Pointer The total-Lagrangian formulation is derived by employing the Cauchy-Born hypothesis. Black-Right-Pointing-Pointer The radial quadrature is used to model the material behavior in surface elements. Black-Right-Pointing-Pointer The quadrature characteristics are derived using the data at the atomistic level.

Real-time simulation of large-scale floods

Science.gov (United States)

Liu, Q.; Qin, Y.; Li, G. D.; Liu, Z.; Cheng, D. J.; Zhao, Y. H.

2016-08-01

According to the complex real-time water situation, the real-time simulation of large-scale floods is very important for flood prevention practice. Model robustness and running efficiency are two critical factors in successful real-time flood simulation. This paper proposed a robust, two-dimensional, shallow water model based on the unstructured Godunov- type finite volume method. A robust wet/dry front method is used to enhance the numerical stability. An adaptive method is proposed to improve the running efficiency. The proposed model is used for large-scale flood simulation on real topography. Results compared to those of MIKE21 show the strong performance of the proposed model.

A Framework for Parallel Numerical Simulations on Multi-Scale Geometries

KAUST Repository

Varduhn, Vasco

2012-06-01

In this paper, an approach on performing numerical multi-scale simulations on fine detailed geometries is presented. In particular, the focus lies on the generation of sufficient fine mesh representations, whereas a resolution of dozens of millions of voxels is inevitable in order to sufficiently represent the geometry. Furthermore, the propagation of boundary conditions is investigated by using simulation results on the coarser simulation scale as input boundary conditions on the next finer scale. Finally, the applicability of our approach is shown on a two-phase simulation for flooding scenarios in urban structures running from a city wide scale to a fine detailed in-door scale on feature rich building geometries. © 2012 IEEE.

The latest full-scale PWR simulator in Japan

International Nuclear Information System (INIS)

Nishimuru, Y.; Tagi, H.; Nakabayashi, T.

2004-01-01

The latest MHI Full-scale Simulator has an excellent system configuration, in both flexibility and extendability, and has highly sophisticated performance in PWR simulation by the adoption of CANAC-II and PRETTY codes. It also has an instructive character to display the plant's internal status, such as RCS condition, through animation. Further, the simulation has been verified to meet a functional examination at model plant, and with a scale model test result in a two-phase flow event, after evaluation for its accuracy. Thus, the Simulator can be devoted to a sophisticated and broad training course on PWR operation. (author)

Atomistic simulation study of short pulse laser interactions with a metal target under conditions of spatial confinement by a transparent overlayer

Energy Technology Data Exchange (ETDEWEB)

Karim, Eaman T.; Shugaev, Maxim; Wu, Chengping; Zhigilei, Leonid V., E-mail: lz2n@virginia.edu [Department of Materials Science and Engineering, University of Virginia, 395 McCormick Road, Charlottesville, Virginia 22904-4745 (United States); Lin, Zhibin; Hainsey, Robert F. [Electro Scientific Industries, Inc., 13900 NW Science Park Drive, Portland, Oregon 97229 (United States)

2014-05-14

The distinct characteristics of short pulse laser interactions with a metal target under conditions of spatial confinement by a solid transparent overlayer are investigated in a series of atomistic simulations. The simulations are performed with a computational model combining classical molecular dynamics (MD) technique with a continuum description of the laser excitation, electron-phonon equilibration, and electronic heat transfer based on two-temperature model (TTM). Two methods for incorporation of the description of a transparent overlayer into the TTM-MD model are designed and parameterized for Ag-silica system. The material response to the laser energy deposition is studied for a range of laser fluences that, in the absence of the transparent overlayer, covers the regimes of melting and resolidification, photomechanical spallation, and phase explosion of the overheated surface region. In contrast to the irradiation in vacuum, the spatial confinement by the overlayer facilitates generation of sustained high-temperature and high-pressure conditions near the metal-overlayer interface, suppresses the generation of unloading tensile wave, decreases the maximum depth of melting, and prevents the spallation and explosive disintegration of the surface region of the metal target. At high laser fluences, when the laser excitation brings the surface region of the metal target to supercritical conditions, the confinement prevents the expansion and phase decomposition characteristic for the vacuum conditions leading to a gradual cooling of the hot compressed supercritical fluid down to the liquid phase and eventual solidification. The target modification in this case is limited to the generation of crystal defects and the detachment of the metal target from the overlayer.

Evaluation of high resolution spatio-temporal precipitation extremes from a stochastic weather generator

DEFF Research Database (Denmark)

Sørup, Hjalte Jomo Danielsen; Christensen, O. B.; Arnbjerg-Nielsen, Karsten

2017-01-01

Spatio-temporal rainfall is modelled for the North-Eastern part of Zealand (Denmark) using the Spatio-Temporal Neyman-Scott Rectangular Pulses model as implemented in the RainSim software. Hourly precipitation series for fitting the model are obtained from a dense network of tipping bucket rain...... gauges in the model area. The spatiotemporal performance of the model with respect to precipitation extremes is evaluated in the points of a 2x2 km regular grid covering the full model area. The model satisfactorily reproduces the extreme behaviour of the observed precipitation with respect to event...... intensity levels and unconditional spatial correlation when evaluated using an event based ranking approach at point scale and an advanced spatiotemporal coupling of extreme events. Prospectively the model can be used as a tool to evaluate the impact of climate change without relying on precipitation output...

Effects of climate change adaptation scenarios on perceived spatio-temporal characteristics of drought events

Science.gov (United States)

Vidal, J.-P.; Martin, E.; Kitova, N.; Najac, J.; Soubeyroux, J.-M.

2012-04-01

Drought events develop in both space and time and they are therefore best described through summary joint spatio-temporal characteristics, like mean duration, mean affected area and total magnitude. This study addresses the issue of future projections of such characteristics of drought events over France through three main research questions: (1) Are downscaled climate projections able to reproduce spatio-temporal characteristics of meteorological and agricultural droughts in France over a present-day period? (2) How such characteristics will evolve over the 21st century under different emissions scenarios? (3) How would perceived drought characteristics evolve under theoretical adaptation scenarios? These questions are addressed using the Isba land surface model, downscaled climate projections from the ARPEGE General Circulation Model under three emissions scenarios, as well as results from a previously performed 50-year multilevel and multiscale drought reanalysis over France (Vidal et al., 2010). Spatio-temporal characteristics of meteorological and agricultural drought events are computed using the Standardized Precipitation Index (SPI) and the Standardized Soil Wetness Index (SSWI), respectively, and for time scales of 3 and 12 months. Results first show that the distributions of joint spatio-temporal characteristics of observed events are well reproduced by the downscaled hydroclimate projections over a present-day period. All spatio-temporal characteristics of drought events are then found to dramatically increase over the 21st century under all considered emissions scenarios, with stronger changes for agricultural droughts. Two theoretical adaptation scenarios are eventually built based on hypotheses of adaptation to evolving climate and hydrological normals. The two scenarios differ by the way the transient adaptation is performed for a given date in the future, with reference to the normals over either the previous 30-year window ("retrospective

Atomic-scale details of dislocation-stacking fault tetrahedra interaction

International Nuclear Information System (INIS)

Osetsky, Yu. N.; Stoller, R.E.; Rodney, D.; Bacon, D.J.

2005-01-01

Stacking fault tetrahedra (SFTs) are formed during irradiation of f.c.c. metals and alloys with low stacking fault energy. The high number density of SFTs observed suggests that they should contribute to radiation-induced hardening and, therefore, be taken into account when estimating mechanical property changes of irradiated materials. Key issue is to describe the interaction between a moving dislocation and an individual SFT, which is characterized by a small physical scale of about 100 nm. In this paper we present results of an atomistic simulation of edge and screw dislocations interacting with small SFTs at different temperatures and strain rates and present mechanisms which can explain the formation of defect-free channels observed experimentally

Atomistic aspects of ductile responses of cubic silicon carbide during nanometric cutting.

Science.gov (United States)

Goel, Saurav; Luo, Xichun; Reuben, Robert L; Rashid, Waleed Bin

2011-11-11

Cubic silicon carbide (SiC) is an extremely hard and brittle material having unique blend of material properties which makes it suitable candidate for microelectromechanical systems and nanoelectromechanical systems applications. Although, SiC can be machined in ductile regime at nanoscale through single-point diamond turning process, the root cause of the ductile response of SiC has not been understood yet which impedes significant exploitation of this ceramic material. In this paper, molecular dynamics simulation has been carried out to investigate the atomistic aspects of ductile response of SiC during nanometric cutting process. Simulation results show that cubic SiC undergoes sp3-sp2 order-disorder transition resulting in the formation of SiC-graphene-like substance with a growth rate dependent on the cutting conditions. The disorder transition of SiC causes the ductile response during its nanometric cutting operations. It was further found out that the continuous abrasive action between the diamond tool and SiC causes simultaneous sp3-sp2 order-disorder transition of diamond tool which results in graphitization of diamond and consequent tool wear.

Visual Data-Analytics of Large-Scale Parallel Discrete-Event Simulations

Energy Technology Data Exchange (ETDEWEB)

Ross, Caitlin; Carothers, Christopher D.; Mubarak, Misbah; Carns, Philip; Ross, Robert; Li, Jianping Kelvin; Ma, Kwan-Liu

2016-11-13

Parallel discrete-event simulation (PDES) is an important tool in the codesign of extreme-scale systems because PDES provides a cost-effective way to evaluate designs of highperformance computing systems. Optimistic synchronization algorithms for PDES, such as Time Warp, allow events to be processed without global synchronization among the processing elements. A rollback mechanism is provided when events are processed out of timestamp order. Although optimistic synchronization protocols enable the scalability of large-scale PDES, the performance of the simulations must be tuned to reduce the number of rollbacks and provide an improved simulation runtime. To enable efficient large-scale optimistic simulations, one has to gain insight into the factors that affect the rollback behavior and simulation performance. We developed a tool for ROSS model developers that gives them detailed metrics on the performance of their large-scale optimistic simulations at varying levels of simulation granularity. Model developers can use this information for parameter tuning of optimistic simulations in order to achieve better runtime and fewer rollbacks. In this work, we instrument the ROSS optimistic PDES framework to gather detailed statistics about the simulation engine. We have also developed an interactive visualization interface that uses the data collected by the ROSS instrumentation to understand the underlying behavior of the simulation engine. The interface connects real time to virtual time in the simulation and provides the ability to view simulation data at different granularities. We demonstrate the usefulness of our framework by performing a visual analysis of the dragonfly network topology model provided by the CODES simulation framework built on top of ROSS. The instrumentation needs to minimize overhead in order to accurately collect data about the simulation performance. To ensure that the instrumentation does not introduce unnecessary overhead, we perform a

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

Science.gov (United States)

McCarty, J; Clark, A J; Copperman, J; Guenza, M G

2014-05-28

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

A transformation theory of stochastic evolution in Red Moon methodology to time evolution of chemical reaction process in the full atomistic system.

Science.gov (United States)

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H 2 + I 2  ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H 2 and I 2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H 2 ] eq and equilibrium constants K eq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H 2 ] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

Spatiotemporal Data Organization and Application Research

Science.gov (United States)

Tan, C.; Yan, S.

2017-09-01

Organization and management of spatiotemporal data is a key support technology for intelligence in all fields of the smart city. The construction of a smart city cannot be realized without spatiotemporal data. Oriented to support intelligent applications this paper proposes an organizational model for spatiotemporal data, and details the construction of a spatiotemporal big data calculation, analysis, and service framework for highly efficient management and intelligent application of spatiotemporal data for the entire data life cycle.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

Science.gov (United States)

2017-01-01

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory. PMID:28475322

Identifying food deserts and swamps based on relative healthy food access: a spatio-temporal Bayesian approach.

Science.gov (United States)

Luan, Hui; Law, Jane; Quick, Matthew

2015-12-30

Obesity and other adverse health outcomes are influenced by individual- and neighbourhood-scale risk factors, including the food environment. At the small-area scale, past research has analysed spatial patterns of food environments for one time period, overlooking how food environments change over time. Further, past research has infrequently analysed relative healthy food access (RHFA), a measure that is more representative of food purchasing and consumption behaviours than absolute outlet density. This research applies a Bayesian hierarchical model to analyse the spatio-temporal patterns of RHFA in the Region of Waterloo, Canada, from 2011 to 2014 at the small-area level. RHFA is calculated as the proportion of healthy food outlets (healthy outlets/healthy + unhealthy outlets) within 4-km from each small-area. This model measures spatial autocorrelation of RHFA, temporal trend of RHFA for the study region, and spatio-temporal trends of RHFA for small-areas. For the study region, a significant decreasing trend in RHFA is observed (-0.024), suggesting that food swamps have become more prevalent during the study period. For small-areas, significant decreasing temporal trends in RHFA were observed for all small-areas. Specific small-areas located in south Waterloo, north Kitchener, and southeast Cambridge exhibited the steepest decreasing spatio-temporal trends and are classified as spatio-temporal food swamps. This research demonstrates a Bayesian spatio-temporal modelling approach to analyse RHFA at the small-area scale. Results suggest that food swamps are more prevalent than food deserts in the Region of Waterloo. Analysing spatio-temporal trends of RHFA improves understanding of local food environment, highlighting specific small-areas where policies should be targeted to increase RHFA and reduce risk factors of adverse health outcomes such as obesity.

Spatiotemporal patterns and predictability of cyberattacks.

Directory of Open Access Journals (Sweden)

Yu-Zhong Chen

Full Text Available A relatively unexplored issue in cybersecurity science and engineering is whether there exist intrinsic patterns of cyberattacks. Conventional wisdom favors absence of such patterns due to the overwhelming complexity of the modern cyberspace. Surprisingly, through a detailed analysis of an extensive data set that records the time-dependent frequencies of attacks over a relatively wide range of consecutive IP addresses, we successfully uncover intrinsic spatiotemporal patterns underlying cyberattacks, where the term "spatio" refers to the IP address space. In particular, we focus on analyzing macroscopic properties of the attack traffic flows and identify two main patterns with distinct spatiotemporal characteristics: deterministic and stochastic. Strikingly, there are very few sets of major attackers committing almost all the attacks, since their attack "fingerprints" and target selection scheme can be unequivocally identified according to the very limited number of unique spatiotemporal characteristics, each of which only exists on a consecutive IP region and differs significantly from the others. We utilize a number of quantitative measures, including the flux-fluctuation law, the Markov state transition probability matrix, and predictability measures, to characterize the attack patterns in a comprehensive manner. A general finding is that the attack patterns possess high degrees of predictability, potentially paving the way to anticipating and, consequently, mitigating or even preventing large-scale cyberattacks using macroscopic approaches.

A study on the plasticity of soda-lime silica glass via molecular dynamics simulations

Science.gov (United States)

Urata, Shingo; Sato, Yosuke

2017-11-01

Molecular dynamics (MD) simulations were applied to construct a plasticity model, which enables one to simulate deformations of soda-lime silica glass (SLSG) by using continuum methods. To model the plasticity, stress induced by uniaxial and a variety of biaxial deformations was measured by MD simulations. We found that the surfaces of yield and maximum stresses, which are evaluated from the equivalent stress-strain curves, are reasonably represented by the Mohr-Coulomb ellipsoid. Comparing a finite element model using the constructed plasticity model to a large scale atomistic model on a nanoindentation simulation of SLSG reveals that the empirical method is accurate enough to evaluate the SLSG mechanical responses. Furthermore, the effect of ion-exchange on the SLSG plasticity was examined by using MD simulations. As a result, it was demonstrated that the effects of the initial compressive stress on the yield and maximum stresses are anisotropic contrary to our expectations.

Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats

Science.gov (United States)

Stalter, S.; Yelash, L.; Emamy, N.; Statt, A.; Hanke, M.; Lukáčová-Medvid'ová, M.; Virnau, P.

2018-03-01

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations typically pose a computational bottleneck, which we investigate in detail in this study. We find that it is preferable to simulate many small systems as opposed to a few large systems, and that a choice of a simple isokinetic thermostat is typically sufficient while thermostats such as Lowe-Andersen allow for simulations at elevated viscosity. We discuss suitable choices for time steps and finite-size effects which arise in the limit of very small simulation boxes. We also argue that if colloidal systems are considered as opposed to atomistic systems, the gap between microscopic and macroscopic simulations regarding time and length scales is significantly smaller. We propose a novel reduced-order technique for the coupling to the macroscopic solver, which allows us to approximate a non-linear stress-strain relation efficiently and thus further reduce computational effort of microscopic simulations.

Atomistic Properties of Solids

CERN Document Server

Sirdeshmukh, Dinker B; Subhadra, K G

2011-01-01

The book deals with atomistic properties of solids which are determined by the crystal structure, interatomic forces and atomic displacements influenced by the effects of temperature, stress and electric fields. The book gives equal importance to experimental details and theory. There are full chapters dedicated to the tensor nature of physical properties, mechanical properties, lattice vibrations, crystal structure determination and ferroelectricity. The other crystalline states like nano-, poly-, liquid- and quasi crystals are discussed. Several new topics like nonlinear optics and the Rietveld method are presented in the book. The book lays emphasis on the role of symmetry in crystal properties. Comprehensiveness is the strength of the book; this allows users at different levels a choice of chapters according to their requirements.

Web-based Visual Analytics for Extreme Scale Climate Science

Energy Technology Data Exchange (ETDEWEB)

Steed, Chad A [ORNL; Evans, Katherine J [ORNL; Harney, John F [ORNL; Jewell, Brian C [ORNL; Shipman, Galen M [ORNL; Smith, Brian E [ORNL; Thornton, Peter E [ORNL; Williams, Dean N. [Lawrence Livermore National Laboratory (LLNL)

2014-01-01

In this paper, we introduce a Web-based visual analytics framework for democratizing advanced visualization and analysis capabilities pertinent to large-scale earth system simulations. We address significant limitations of present climate data analysis tools such as tightly coupled dependencies, ineffi- cient data movements, complex user interfaces, and static visualizations. Our Web-based visual analytics framework removes critical barriers to the widespread accessibility and adoption of advanced scientific techniques. Using distributed connections to back-end diagnostics, we minimize data movements and leverage HPC platforms. We also mitigate system dependency issues by employing a RESTful interface. Our framework embraces the visual analytics paradigm via new visual navigation techniques for hierarchical parameter spaces, multi-scale representations, and interactive spatio-temporal data mining methods that retain details. Although generalizable to other science domains, the current work focuses on improving exploratory analysis of large-scale Community Land Model (CLM) and Community Atmosphere Model (CAM) simulations.

Comparison of continuum and atomistic methods for the analysis of InAs/GaAs quantum dots

DEFF Research Database (Denmark)

Barettin, D.; Pecchia, A.; Penazzi, G.

2011-01-01

We present a comparison of continuum k · p and atomistic empirical Tight Binding methods for the analysis of the optoelectronic properties of InAs/GaAs quantum dots.......We present a comparison of continuum k · p and atomistic empirical Tight Binding methods for the analysis of the optoelectronic properties of InAs/GaAs quantum dots....

Analyzing and Driving Cluster Formation in Atomistic Simulations.

Science.gov (United States)

Tribello, Gareth A; Giberti, Federico; Sosso, Gabriele C; Salvalaglio, Matteo; Parrinello, Michele

2017-03-14

In this paper a set of computational tools for identifying the phases contained in a system composed of atoms or molecules is introduced. The method is rooted in graph theory and combines atom centered symmetry functions, adjacency matrices, and clustering algorithms to identify regions of space where the properties of the system constituents can be considered uniform. We show how this method can be used to define collective variables and how these collective variables can be used to enhance the sampling of nucleation events. We then show how this method can be used to analyze simulations of crystal nucleation and growth by using it to analyze simulations of the nucleation of the molecular crystal urea and simulations of nucleation in a semiconducting alloy. The semiconducting alloy example we discuss is particular challenging as multiple nucleation centers are formed. We show, however, that our algorithm is able to detect the grain boundaries in the resulting polycrystal.

Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

Science.gov (United States)

Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

2017-02-01

The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

Effective and efficient analysis of spatio-temporal data

Science.gov (United States)

Zhang, Zhongnan

Spatio-temporal data mining, i.e., mining knowledge from large amount of spatio-temporal data, is a highly demanding field because huge amounts of spatio-temporal data have been collected in various applications, ranging from remote sensing, to geographical information systems (GIS), computer cartography, environmental assessment and planning, etc. The collection data far exceeded human's ability to analyze which make it crucial to develop analysis tools. Recent studies on data mining have extended to the scope of data mining from relational and transactional datasets to spatial and temporal datasets. Among the various forms of spatio-temporal data, remote sensing images play an important role, due to the growing wide-spreading of outer space satellites. In this dissertation, we proposed two approaches to analyze the remote sensing data. The first one is about applying association rules mining onto images processing. Each image was divided into a number of image blocks. We built a spatial relationship for these blocks during the dividing process. This made a large number of images into a spatio-temporal dataset since each image was shot in time-series. The second one implemented co-occurrence patterns discovery from these images. The generated patterns represent subsets of spatial features that are located together in space and time. A weather analysis is composed of individual analysis of several meteorological variables. These variables include temperature, pressure, dew point, wind, clouds, visibility and so on. Local-scale models provide detailed analysis and forecasts of meteorological phenomena ranging from a few kilometers to about 100 kilometers in size. When some of above meteorological variables have some special change tendency, some kind of severe weather will happen in most cases. Using the discovery of association rules, we found that some special meteorological variables' changing has tight relation with some severe weather situation that will happen

Multi-Contextual Segregation and Environmental Justice Research: Toward Fine-Scale Spatiotemporal Approaches.

Science.gov (United States)

Park, Yoo Min; Kwan, Mei-Po

2017-10-10

Many environmental justice studies have sought to examine the effect of residential segregation on unequal exposure to environmental factors among different social groups, but little is known about how segregation in non-residential contexts affects such disparity. Based on a review of the relevant literature, this paper discusses the limitations of traditional residence-based approaches in examining the association between socioeconomic or racial/ethnic segregation and unequal environmental exposure in environmental justice research. It emphasizes that future research needs to go beyond residential segregation by considering the full spectrum of segregation experienced by people in various geographic and temporal contexts of everyday life. Along with this comprehensive understanding of segregation, the paper also highlights the importance of assessing environmental exposure at a high spatiotemporal resolution in environmental justice research. The successful integration of a comprehensive concept of segregation, high-resolution data and fine-grained spatiotemporal approaches to assessing segregation and environmental exposure would provide more nuanced and robust findings on the associations between segregation and disparities in environmental exposure and their health impacts. Moreover, it would also contribute to significantly expanding the scope of environmental justice research.

Multi-Contextual Segregation and Environmental Justice Research: Toward Fine-Scale Spatiotemporal Approaches

Directory of Open Access Journals (Sweden)

Yoo Min Park

2017-10-01

Full Text Available Many environmental justice studies have sought to examine the effect of residential segregation on unequal exposure to environmental factors among different social groups, but little is known about how segregation in non-residential contexts affects such disparity. Based on a review of the relevant literature, this paper discusses the limitations of traditional residence-based approaches in examining the association between socioeconomic or racial/ethnic segregation and unequal environmental exposure in environmental justice research. It emphasizes that future research needs to go beyond residential segregation by considering the full spectrum of segregation experienced by people in various geographic and temporal contexts of everyday life. Along with this comprehensive understanding of segregation, the paper also highlights the importance of assessing environmental exposure at a high spatiotemporal resolution in environmental justice research. The successful integration of a comprehensive concept of segregation, high-resolution data and fine-grained spatiotemporal approaches to assessing segregation and environmental exposure would provide more nuanced and robust findings on the associations between segregation and disparities in environmental exposure and their health impacts. Moreover, it would also contribute to significantly expanding the scope of environmental justice research.

Atomistic Kinetic Monte Carlo studies of microchemical evolutions driven by diffusion processes under irradiation

Science.gov (United States)

Soisson, F.; Becquart, C. S.; Castin, N.; Domain, C.; Malerba, L.; Vincent, E.

2010-11-01

Atomistic Kinetic Monte Carlo (AKMC) simulations are a powerful tool to study the microstructural and microchemical evolution of alloys controlled by diffusion processes, under irradiation and during thermal ageing. In the framework of the FP6 Perfect program, two main approaches have been applied to binary and multicomponent iron based alloys. The first one is based on a diffusion model which takes into account vacancy and self-interstitial jumps, using simple rigid lattice approximation and broken-bond models to compute the point-defect jump frequencies. The corresponding parameters are fitted on ab initio calculations of a few typical configurations and migration barriers. The second method uses empirical potentials to compute a much larger number of migration barriers, including atomic relaxations, and Artificial Intelligence regression methods to predict the other ones. It is somewhat less rapid than the first one, but significantly more than simulations using "on-the-fly" calculations of all the barriers. We review here the recent advances and perspectives concerning these techniques.

Atomistic Kinetic Monte Carlo studies of microchemical evolutions driven by diffusion processes under irradiation

International Nuclear Information System (INIS)

Soisson, F.; Becquart, C.S.; Castin, N.; Domain, C.; Malerba, L.; Vincent, E.

2010-01-01

Atomistic Kinetic Monte Carlo (AKMC) simulations are a powerful tool to study the microstructural and microchemical evolution of alloys controlled by diffusion processes, under irradiation and during thermal ageing. In the framework of the FP6 Perfect program, two main approaches have been applied to binary and multicomponent iron based alloys. The first one is based on a diffusion model which takes into account vacancy and self-interstitial jumps, using simple rigid lattice approximation and broken-bond models to compute the point-defect jump frequencies. The corresponding parameters are fitted on ab initio calculations of a few typical configurations and migration barriers. The second method uses empirical potentials to compute a much larger number of migration barriers, including atomic relaxations, and Artificial Intelligence regression methods to predict the other ones. It is somewhat less rapid than the first one, but significantly more than simulations using 'on-the-fly' calculations of all the barriers. We review here the recent advances and perspectives concerning these techniques.

Coupling biomechanics to a cellular level model: an approach to patient-specific image driven multi-scale and multi-physics tumor simulation.

Science.gov (United States)

May, Christian P; Kolokotroni, Eleni; Stamatakos, Georgios S; Büchler, Philippe

2011-10-01

Modeling of tumor growth has been performed according to various approaches addressing different biocomplexity levels and spatiotemporal scales. Mathematical treatments range from partial differential equation based diffusion models to rule-based cellular level simulators, aiming at both improving our quantitative understanding of the underlying biological processes and, in the mid- and long term, constructing reliable multi-scale predictive platforms to support patient-individualized treatment planning and optimization. The aim of this paper is to establish a multi-scale and multi-physics approach to tumor modeling taking into account both the cellular and the macroscopic mechanical level. Therefore, an already developed biomodel of clinical tumor growth and response to treatment is self-consistently coupled with a biomechanical model. Results are presented for the free growth case of the imageable component of an initially point-like glioblastoma multiforme tumor. The composite model leads to significant tumor shape corrections that are achieved through the utilization of environmental pressure information and the application of biomechanical principles. Using the ratio of smallest to largest moment of inertia of the tumor material to quantify the effect of our coupled approach, we have found a tumor shape correction of 20% by coupling biomechanics to the cellular simulator as compared to a cellular simulation without preferred growth directions. We conclude that the integration of the two models provides additional morphological insight into realistic tumor growth behavior. Therefore, it might be used for the development of an advanced oncosimulator focusing on tumor types for which morphology plays an important role in surgical and/or radio-therapeutic treatment planning. Copyright © 2011 Elsevier Ltd. All rights reserved.

Short-term spatio-temporal wind power forecast in robust look-ahead power system dispatch

KAUST Repository

Xie, Le

2014-01-01

We propose a novel statistical wind power forecast framework, which leverages the spatio-temporal correlation in wind speed and direction data among geographically dispersed wind farms. Critical assessment of the performance of spatio-temporal wind power forecast is performed using realistic wind farm data from West Texas. It is shown that spatio-temporal wind forecast models are numerically efficient approaches to improving forecast quality. By reducing uncertainties in near-term wind power forecasts, the overall cost benefits on system dispatch can be quantified. We integrate the improved forecast with an advanced robust look-ahead dispatch framework. This integrated forecast and economic dispatch framework is tested in a modified IEEE RTS 24-bus system. Numerical simulation suggests that the overall generation cost can be reduced by up to 6% using a robust look-ahead dispatch coupled with spatio-temporal wind forecast as compared with persistent wind forecast models. © 2013 IEEE.

Spatio-temporal correlations in models of collective motion ruled by different dynamical laws.

Science.gov (United States)

Cavagna, Andrea; Conti, Daniele; Giardina, Irene; Grigera, Tomas S; Melillo, Stefania; Viale, Massimiliano

2016-11-15

Information transfer is an essential factor in determining the robustness of biological systems with distributed control. The most direct way to study the mechanisms ruling information transfer is to experimentally observe the propagation across the system of a signal triggered by some perturbation. However, this method may be inefficient for experiments in the field, as the possibilities to perturb the system are limited and empirical observations must rely on natural events. An alternative approach is to use spatio-temporal correlations to probe the information transfer mechanism directly from the spontaneous fluctuations of the system, without the need to have an actual propagating signal on record. Here we test this method on models of collective behaviour in their deeply ordered phase by using ground truth data provided by numerical simulations in three dimensions. We compare two models characterized by very different dynamical equations and information transfer mechanisms: the classic Vicsek model, describing an overdamped noninertial dynamics and the inertial spin model, characterized by an underdamped inertial dynamics. By using dynamic finite-size scaling, we show that spatio-temporal correlations are able to distinguish unambiguously the diffusive information transfer mechanism of the Vicsek model from the linear mechanism of the inertial spin model.

Multiscale Simulation of Thermo-mechanical Processes in Irradiated Fission-reactor Materials

International Nuclear Information System (INIS)

Phillpot, Simon R.

2012-01-01

The work funded from this project has been published in six papers, with two more in draft form, with submission planned for the near future. The papers are: (1) Kinetically-Evolving Irradiation-Induced Point-Defect Clusters in UO 2 by Molecular-Dynamics Simulation; (2) Kinetically driven point-defect clustering in irradiated MgO by molecular-dynamics simulation; (3) Grain-Boundary Source/Sink Behavior for Point Defect: An Atomistic Simulation Study; (4) Energetics of intrinsic point defects in uranium dioxide from electronic structure calculations; (5) Thermodynamics of fission products in UO 2±x ; and (6) Atomistic study of grain boundary sink strength under prolonged electron irradiation. The other two pieces of work that are currently being written-up for publication are: (1) Effect of Pores and He Bubbles on the Thermal Transport Properties of UO2 by Molecular Dynamics Simulation; and (2) Segregation of Ruthenium to Edge Dislocations in Uranium Dioxide.

Hierarchical Bayesian modeling of spatio-temporal patterns of lung cancer incidence risk in Georgia, USA: 2000-2007

Science.gov (United States)

Yin, Ping; Mu, Lan; Madden, Marguerite; Vena, John E.

2014-10-01

Lung cancer is the second most commonly diagnosed cancer in both men and women in Georgia, USA. However, the spatio-temporal patterns of lung cancer risk in Georgia have not been fully studied. Hierarchical Bayesian models are used here to explore the spatio-temporal patterns of lung cancer incidence risk by race and gender in Georgia for the period of 2000-2007. With the census tract level as the spatial scale and the 2-year period aggregation as the temporal scale, we compare a total of seven Bayesian spatio-temporal models including two under a separate modeling framework and five under a joint modeling framework. One joint model outperforms others based on the deviance information criterion. Results show that the northwest region of Georgia has consistently high lung cancer incidence risk for all population groups during the study period. In addition, there are inverse relationships between the socioeconomic status and the lung cancer incidence risk among all Georgian population groups, and the relationships in males are stronger than those in females. By mapping more reliable variations in lung cancer incidence risk at a relatively fine spatio-temporal scale for different Georgian population groups, our study aims to better support healthcare performance assessment, etiological hypothesis generation, and health policy making.

Transient spatiotemporal chaos in the Morris-Lecar neuronal ring network

Energy Technology Data Exchange (ETDEWEB)

Keplinger, Keegan, E-mail: keegankeplinger@gmail.com; Wackerbauer, Renate, E-mail: rawackerbauer@alaska.edu [Department of Physics, University of Alaska, Fairbanks, Alaska 99775-5920 (United States)

2014-03-15

Transient behavior is thought to play an integral role in brain functionality. Numerical simulations of the firing activity of diffusively coupled, excitable Morris-Lecar neurons reveal transient spatiotemporal chaos in the parameter regime below the saddle-node on invariant circle bifurcation point. The neighborhood of the chaotic saddle is reached through perturbations of the rest state, in which few initially active neurons at an effective spatial distance can initiate spatiotemporal chaos. The system escapes from the neighborhood of the chaotic saddle to either the rest state or to a state of pulse propagation. The lifetime of the chaotic transients is manipulated in a statistical sense through a singular application of a synchronous perturbation to a group of neurons.

Transient spatiotemporal chaos in the Morris-Lecar neuronal ring network.

Science.gov (United States)

Keplinger, Keegan; Wackerbauer, Renate

2014-03-01

Transient behavior is thought to play an integral role in brain functionality. Numerical simulations of the firing activity of diffusively coupled, excitable Morris-Lecar neurons reveal transient spatiotemporal chaos in the parameter regime below the saddle-node on invariant circle bifurcation point. The neighborhood of the chaotic saddle is reached through perturbations of the rest state, in which few initially active neurons at an effective spatial distance can initiate spatiotemporal chaos. The system escapes from the neighborhood of the chaotic saddle to either the rest state or to a state of pulse propagation. The lifetime of the chaotic transients is manipulated in a statistical sense through a singular application of a synchronous perturbation to a group of neurons.

Towards large scale stochastic rainfall models for flood risk assessment in trans-national basins

Science.gov (United States)

Serinaldi, F.; Kilsby, C. G.

2012-04-01

While extensive research has been devoted to rainfall-runoff modelling for risk assessment in small and medium size watersheds, less attention has been paid, so far, to large scale trans-national basins, where flood events have severe societal and economic impacts with magnitudes quantified in billions of Euros. As an example, in the April 2006 flood events along the Danube basin at least 10 people lost their lives and up to 30 000 people were displaced, with overall damages estimated at more than half a billion Euros. In this context, refined analytical methods are fundamental to improve the risk assessment and, then, the design of structural and non structural measures of protection, such as hydraulic works and insurance/reinsurance policies. Since flood events are mainly driven by exceptional rainfall events, suitable characterization and modelling of space-time properties of rainfall fields is a key issue to perform a reliable flood risk analysis based on alternative precipitation scenarios to be fed in a new generation of large scale rainfall-runoff models. Ultimately, this approach should be extended to a global flood risk model. However, as the need of rainfall models able to account for and simulate spatio-temporal properties of rainfall fields over large areas is rather new, the development of new rainfall simulation frameworks is a challenging task involving that faces with the problem of overcoming the drawbacks of the existing modelling schemes (devised for smaller spatial scales), but keeping the desirable properties. In this study, we critically summarize the most widely used approaches for rainfall simulation. Focusing on stochastic approaches, we stress the importance of introducing suitable climate forcings in these simulation schemes in order to account for the physical coherence of rainfall fields over wide areas. Based on preliminary considerations, we suggest a modelling framework relying on the Generalized Additive Models for Location, Scale

An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations

Science.gov (United States)

Bernal, M. A.; Sikansi, D.; Cavalcante, F.; Incerti, S.; Champion, C.; Ivanchenko, V.; Francis, Z.

2013-12-01

In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model. Catalogue identifier: AEPZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1245 No. of bytes in distributed program, including test data, etc.: 6574 Distribution format: tar.gz Programming language: FORTRAN. Computer: Any. Operating system: Multi-platform. RAM: 2 Gb Classification: 3. Nature of problem: The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Solution method: This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30 nm chromatin fiber. This subroutine carries out a series of coordinate transformations

Objective spatiotemporal proxy-model comparisons of the Asian monsoon for the last millennium

Science.gov (United States)

Anchukaitis, K. J.; Cook, E. R.; Ammann, C. M.; Buckley, B. M.; D'Arrigo, R. D.; Jacoby, G.; Wright, W. E.; Davi, N.; Li, J.

2008-12-01

The Asian monsoon system can be studied using a complementary proxy/simulation approach which evaluates climate models using estimates of past precipitation and temperature, and which subsequently applies the best understanding of the physics of the climate system as captured in general circulation models to evaluate the broad-scale dynamics behind regional paleoclimate reconstructions. Here, we use a millennial-length climate field reconstruction of monsoon season summer (JJA) drought, developed from tree- ring proxies, with coupled climate simulations from NCAR CSM1.4 and CCSM3 to evaluate the cause of large- scale persistent droughts over the last one thousand years. Direct comparisons are made between the external forced response within the climate model and the spatiotemporal field reconstruction. In order to identify patterns of drought associated with internal variability in the climate system, we use a model/proxy analog technique which objectively selects epochs in the model that most closely reproduce those observed in the reconstructions. The concomitant ocean-atmosphere dynamics are then interpreted in order to identify and understand the internal climate system forcing of low frequency monsoon variability. We examine specific periods of extensive or intensive regional drought in the 15th, 17th, and 18th centuries, many of which are coincident with major cultural changes in the region.

A novel method for one-way hash function construction based on spatiotemporal chaos

Energy Technology Data Exchange (ETDEWEB)

Ren Haijun [College of Software Engineering, Chongqing University, Chongqing 400044 (China); State Key Laboratory of Power Transmission Equipment and System Security and New Technology, Chongqing University, Chongqing 400044 (China)], E-mail: jhren@cqu.edu.cn; Wang Yong; Xie Qing [Key Laboratory of Electronic Commerce and Logistics of Chongqing, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China); Yang Huaqian [Department of Computer and Modern Education Technology, Chongqing Education of College, Chongqing 400067 (China)

2009-11-30

A novel hash algorithm based on a spatiotemporal chaos is proposed. The original message is first padded with zeros if needed. Then it is divided into a number of blocks each contains 32 bytes. In the hashing process, each block is partitioned into eight 32-bit values and input into the spatiotemporal chaotic system. Then, after iterating the system for four times, the next block is processed by the same way. To enhance the confusion and diffusion effect, the cipher block chaining (CBC) mode is adopted in the algorithm. The hash value is obtained from the final state value of the spatiotemporal chaotic system. Theoretic analyses and numerical simulations both show that the proposed hash algorithm possesses good statistical properties, strong collision resistance and high efficiency, as required by practical keyed hash functions.

A novel method for one-way hash function construction based on spatiotemporal chaos

International Nuclear Information System (INIS)

Ren Haijun; Wang Yong; Xie Qing; Yang Huaqian

2009-01-01

A novel hash algorithm based on a spatiotemporal chaos is proposed. The original message is first padded with zeros if needed. Then it is divided into a number of blocks each contains 32 bytes. In the hashing process, each block is partitioned into eight 32-bit values and input into the spatiotemporal chaotic system. Then, after iterating the system for four times, the next block is processed by the same way. To enhance the confusion and diffusion effect, the cipher block chaining (CBC) mode is adopted in the algorithm. The hash value is obtained from the final state value of the spatiotemporal chaotic system. Theoretic analyses and numerical simulations both show that the proposed hash algorithm possesses good statistical properties, strong collision resistance and high efficiency, as required by practical keyed hash functions.

Synchronization of spatiotemporal chaotic systems and application to secure communication of digital image

International Nuclear Information System (INIS)

Wang Xing-Yuan; Zhang Na; Ren Xiao-Li; Zhang Yong-Lei

2011-01-01

Coupled map lattices (CMLs) are taken as examples to study the synchronization of spatiotemporal chaotic systems. In this paper, we use the nonlinear coupled method to implement the synchronization of two coupled map lattices. Through the appropriate separation of the linear term from the nonlinear term of the spatiotemporal chaotic system, we set the nonlinear term as the coupling function and then we can achieve the synchronization of two coupled map lattices. After that, we implement the secure communication of digital image using this synchronization method. Then, the discrete characteristics of the nonlinear coupling spatiotemporal chaos are applied to the discrete pixel of the digital image. After the synchronization of both the communication parties, the receiver can decrypt the original image. Numerical simulations show the effectiveness and the feasibility of the proposed program. (general)

Formalizing Knowledge in Multi-Scale Agent-Based Simulations.

Science.gov (United States)

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.

Multiscale modeling of polyisoprene on graphite

International Nuclear Information System (INIS)

Pandey, Yogendra Narayan; Brayton, Alexander; Doxastakis, Manolis; Burkhart, Craig; Papakonstantopoulos, George J.

2014-01-01

The local dynamics and the conformational properties of polyisoprene next to a smooth graphite surface constructed by graphene layers are studied by a multiscale methodology. First, fully atomistic molecular dynamics simulations of oligomers next to the surface are performed. Subsequently, Monte Carlo simulations of a systematically derived coarse-grained model generate numerous uncorrelated structures for polymer systems. A new reverse backmapping strategy is presented that reintroduces atomistic detail. Finally, multiple extensive fully atomistic simulations with large systems of long macromolecules are employed to examine local dynamics in proximity to graphite. Polyisoprene repeat units arrange close to a parallel configuration with chains exhibiting a distribution of contact lengths. Efficient Monte Carlo algorithms with the coarse-grain model are capable of sampling these distributions for any molecular weight in quantitative agreement with predictions from atomistic models. Furthermore, molecular dynamics simulations with well-equilibrated systems at all length-scales support an increased dynamic heterogeneity that is emerging from both intermolecular interactions with the flat surface and intramolecular cooperativity. This study provides a detailed comprehensive picture of polyisoprene on a flat surface and consists of an effort to characterize such systems in atomistic detail

Spontaneous Formation of A Nanotube From A Square Ag Nanowire: An Atomistic View

Science.gov (United States)

Konuk Onat, Mine; Durukanoglu, Sondan

2012-02-01

We have performed molecular static calculations to investigate the recently observed phenomenon of the spontaneous formation of a nanotube from a regular, square Ag nanowire[1]. In the simulations, atoms are allowed to interact via the model potential obtained from the modified embedded atom method. Our simulations predict that this particular type of structural phase transformation is controlled by the nature of applied strain, length of the wire and initial cross-sectional shape. For such a perfect structural transformation, the axially oriented fcc nanowire needs (1) to be formed by stacking A and B layers of an fcc crystal, both possessing the geometry of two interpenetrating one-lattice-parameter-wide squares, containing four atoms each, (2) to have an optimum length of eight layers, and (3) to be exposed to a combination of low and high stress along the length direction. The results further offer insights into atomistic nature of this specific structural transformation into a nanotube with the smallest possible cross-section. [1] M.J. Lagos et al., Nature Nanotech. 4, 149 (2009).

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

Science.gov (United States)

Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D.

2016-08-01

This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

Directory of Open Access Journals (Sweden)

Thomas M. Vlasic

2016-08-01

Full Text Available This work uses density functional theory (DFT to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane, at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

Energy Technology Data Exchange (ETDEWEB)

Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D., E-mail: alejandro.rey@mcgill.ca [Department of Chemical Engineering, McGill University, Montreal H3A 0C5 (Canada)

2016-08-15

This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

Fast Simulation of Large-Scale Floods Based on GPU Parallel Computing

OpenAIRE

Qiang Liu; Yi Qin; Guodong Li

2018-01-01

Computing speed is a significant issue of large-scale flood simulations for real-time response to disaster prevention and mitigation. Even today, most of the large-scale flood simulations are generally run on supercomputers due to the massive amounts of data and computations necessary. In this work, a two-dimensional shallow water model based on an unstructured Godunov-type finite volume scheme was proposed for flood simulation. To realize a fast simulation of large-scale floods on a personal...

Analysis of Spatiotemporal Statistical Properties of Rainfall in the Phoenix Metropolitan Area

Science.gov (United States)

Mascaro, G.

2016-12-01

The analysis of the rainfall statistical properties at multiple spatiotemporal scales is a necessary preliminary step to support modeling of urban hydrology, including flood prediction and simulation of impacts of land use changes. In this contribution, the rainfall statistical properties are analyzed in the Phoenix Metropolitan area and its surroundings ( 29600 km2) in Arizona using observations from 310 gauges of the Flood Control District of the Maricopa County network. Different techniques are applied to investigate the rainfall properties at temporal scales from 1 min to years and to quantify the associated spatial variability. Results reveal the following. The rainfall regime is characterized by high interannual variability, which is partially explained by teleconnections with El Niño Southern Oscillation, and marked seasonality, with two maxima in the monsoon season from July to September and in winter from November to March. Elevation has a significant control on seasonal rainfall accumulation, strength of thermal convective activity during the monsoon, and peak occurrence of the rainfall diurnal cycle present in summer. The spatial correlation of wintertime rainfall is high even at short aggregation times (cells).

Impact of Spatiotemporal Characteristics of Rainfall Inputs on Integrated Catchment Dissolved Oxygen Simulations

Directory of Open Access Journals (Sweden)

Antonio M. Moreno-Rodenas

2017-11-01

Full Text Available Integrated Catchment Modelling aims to simulate jointly urban drainage systems, wastewater treatment plant and rivers. The effect of rainfall input uncertainties in the modelling of individual urban drainage systems has been discussed in several studies already. However, this influence changes when simultaneously simulating several urban drainage subsystems and their impact on receiving water quality. This study investigates the effect of the characteristics of rainfall inputs on a large-scale integrated catchment simulator for dissolved oxygen predictions in the River Dommel (The Netherlands. Rainfall products were generated with varying time-aggregation (10, 30 and 60 min deriving from different sources of data with increasing spatial information: (1 Homogeneous rainfall from a single rain gauge; (2 block kriging from 13 rain gauges; (3 averaged C-Band radar estimation and (4 kriging with external drift combining radar and rain gauge data with change of spatial support. The influence of the different rainfall inputs was observed at combined sewer overflows (CSO and dissolved oxygen (DO dynamics in the river. Comparison of the simulations with river monitoring data showed a low sensitivity to temporal aggregation of rainfall inputs and a relevant impact of the spatial scale with a link to the storm characteristics to CSO and DO concentration in the receiving water.

Bayesian spatiotemporal model of fMRI data using transfer functions.

Science.gov (United States)

Quirós, Alicia; Diez, Raquel Montes; Wilson, Simon P

2010-09-01

This research describes a new Bayesian spatiotemporal model to analyse BOLD fMRI studies. In the temporal dimension, we describe the shape of the hemodynamic response function (HRF) with a transfer function model. The spatial continuity and local homogeneity of the evoked responses are modelled by a Gaussian Markov random field prior on the parameter indicating activations. The proposal constitutes an extension of the spatiotemporal model presented in a previous approach [Quirós, A., Montes Diez, R. and Gamerman, D., 2010. Bayesian spatiotemporal model of fMRI data, Neuroimage, 49: 442-456], offering more flexibility in the estimation of the HRF and computational advantages in the resulting MCMC algorithm. Simulations from the model are performed in order to ascertain the performance of the sampling scheme and the ability of the posterior to estimate model parameters, as well as to check the model sensitivity to signal to noise ratio. Results are shown on synthetic data and on a real data set from a block-design fMRI experiment. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Global-Scale Associations of Vegetation Phenology with Rainfall and Temperature at a High Spatio-Temporal Resolution

Directory of Open Access Journals (Sweden)

Nicholas Clinton

2014-08-01

Full Text Available Phenology response to climatic variables is a vital indicator for understanding changes in biosphere processes as related to possible climate change. We investigated global phenology relationships to precipitation and land surface temperature (LST at high spatial and temporal resolution for calendar years 2008–2011. We used cross-correlation between MODIS Enhanced Vegetation Index (EVI, MODIS LST and Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN gridded rainfall to map phenology relationships at 1-km spatial resolution and weekly temporal resolution. We show these data to be rich in spatiotemporal information, illustrating distinct phenology patterns as a result of complex overlapping gradients of climate, ecosystem and land use/land cover. The data are consistent with broad-scale, coarse-resolution modeled ecosystem limitations to moisture, temperature and irradiance. We suggest that high-resolution phenology data are useful as both an input and complement to land use/land cover classifiers and for understanding climate change vulnerability in natural and anthropogenic landscapes.

Spatio-Temporal Saliency Perception via Hypercomplex Frequency Spectral Contrast

Directory of Open Access Journals (Sweden)

Zhiqiang Tian

2013-03-01

Full Text Available Salient object perception is the process of sensing the salient information from the spatio-temporal visual scenes, which is a rapid pre-attention mechanism for the target location in a visual smart sensor. In recent decades, many successful models of visual saliency perception have been proposed to simulate the pre-attention behavior. Since most of the methods usually need some ad hoc parameters or high-cost preprocessing, they are difficult to rapidly detect salient object or be implemented by computing parallelism in a smart sensor. In this paper, we propose a novel spatio-temporal saliency perception method based on spatio-temporal hypercomplex spectral contrast (HSC. Firstly, the proposed HSC algorithm represent the features in the HSV (hue, saturation and value color space and features of motion by a hypercomplex number. Secondly, the spatio-temporal salient objects are efficiently detected by hypercomplex Fourier spectral contrast in parallel. Finally, our saliency perception model also incorporates with the non-uniform sampling, which is a common phenomenon of human vision that directs visual attention to the logarithmic center of the image/video in natural scenes. The experimental results on the public saliency perception datasets demonstrate the effectiveness of the proposed approach compared to eleven state-of-the-art approaches. In addition, we extend the proposed model to moving object extraction in dynamic scenes, and the proposed algorithm is superior to the traditional algorithms.

The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.

Science.gov (United States)

Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele

2017-09-14

In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.

Molecular Simulation Studies of Covalently and Ionically Grafted Nanoparticles

Science.gov (United States)

Hong, Bingbing

Solvent-free covalently- or ionically-grafted nanoparticles (CGNs and IGNs) are a new class of organic-inorganic hybrid composite materials exhibiting fluid-like behaviors around room temperature. With similar structures to prior systems, e.g. nanocomposites, neutral or charged colloids, ionic liquids, etc, CGNs and IGNs inherit the functionality of inorganic nanopariticles, the facile processibility of polymers, as well as conductivity and nonvolatility from their constituent materials. In spite of the extensive prior experimental research having covered synthesis and measurements of thermal and dynamic properties, little progress in understanding of these new materials at the molecular level has been achieved, because of the lack of simulation work in this new area. Atomistic and coarse-grained molecular dynamics simulations have been performed in this thesis to investigate the thermodynamics, structure, and dynamics of these systems and to seek predictive methods predictable for their properties. Starting from poly(ethylene oxide) oligomers (PEO) melts, we established atomistic models based on united-atom representations of methylene. The Green-Kubo and Einstein-Helfand formulas were used to calculate the transport properties. The simulations generate densities, viscosities, diffusivities, in good agreement with experimental data. The chain-length dependence of the transport properties suggests that neither Rouse nor reptation models are applicable in the short-chain regime investigated. Coupled with thermodynamic integration methods, the models give good predictions of pressure-composition-density relations for CO 2 + PEO oligomers. Water effects on the Henry's constant of CO 2 in PEO have also been investigated. The dependence of the calculated Henry's constants on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. CGNs are modeled by the inclusion of solid-sphere nanoparticles into the atomistic