Top PDF Atomistic Simulations of Materials: Methods for Accurate Potentials and Realistic Time-Scales

Atomistic Simulations of Materials: Methods for Accurate Potentials and Realistic Time-Scales

Atomistic Simulations of Materials: Methods for Accurate Potentials and Realistic Time-Scales

It has remained an unsolved problem so far to design and perform fully atomistic simu- lations that could provide a picture of temperature dependent activation free energies of dislocation nucleation from surfaces at realistic loads and loading rates. Such a picture is key to linking experimental results with simulation predictions [87,106,117]. The critical nucleus for surface nucleation can be as small as a few atomic planes, thus questioning the applicability of continuum methods. As for classical MD, the time-scale achievable is several orders of magnitude smaller than experiments, thus limiting MD simulations to regimes of extremely high nucleation rates. With our recently proposed hybrid MC-MD method that allows us to achieve extended time- scales while still maintaining atomistic resolution, we are able to study the temper- ature dependence of activation parameters for surface nucleation of dislocations in pristine nanowires and obtain several significant results in an activation regime actu- ally achievable in laboratory experiments. The specific problem we consider pertains to several nano-indentation experiments where it was found that even if the applied stress on a sample is in the elastic regime, yielding could occur after a certain statis- tically distributed waiting time [118–120]. We perform fully atomistic simulations of this time-dependent incipient plasticity behavior in gold nanowires, reaching hundreds of milliseconds time-scales for several thousand atoms. After collecting statistics for various temperatures and applied stresses, we then derive the full picture of stress and temperature dependence of the activation free energy.
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Large-scale multiscale modeling of phase transformation in nanocrystalline materials: Atomistic and Phase-Field methods

Large-scale multiscale modeling of phase transformation in nanocrystalline materials: Atomistic and Phase-Field methods

In order to compare different microstructures at dif- ferent phase-transformation temperatures quantitatively for atomistic (MD) and mesoscopic (phase-field) ap- proaches, the grain diameter versus square root of phase- transformation time is plotted in Figure 11. Note that the diagrams in Figure 11 are plotted after 100 ps due to reaching convergence plateu of temperature, pair-wise energy, and total energy according to Figures 3 to 5. Due to Figure 11, it could be understood that phase-field sim- ulation result of grain size is close to grain size evolution of atomistic simulations at 700K for all the initial mi- crostructure configurations. In fact, this approach could be used to extract kinetic variables of phase-field (meso- scopic) approach at different temperature by matching the grain diameter evolution with molecular dynamics results. The most accurate agreement between molecu- lar dynamics and phase-field simulations is observed at grain diameter evolution diagram of initial 9 grains struc- ture at 700K, which means the kinetic variables that are extracted from [2–4] could capture phase-transformation behavior of pure Aluminum at 700K precisely. At the end, it could be noted that based on findings from Fig- ure 11, it could be inferred that molecular dynamics pro- pose much more flexible computational framework, which could capture different phase-transformation regimes of nanocrystalline materials more precisely [34].
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Molecular Simulations of Protein-Induced Membrane Remodeling

Molecular Simulations of Protein-Induced Membrane Remodeling

The most straightforward way to improve the sampling of a molecular dynamics simulation is to simulate multiple copies of the same system using slightly different starting configurations. This provides a more robust sample, albeit at the same cost as the original simulation. To efficiently extend the atomistic methodology to longer time-scales, a collection of enhanced sampling methods have been developed. For ex- ample, graph-based geometric methods, probabilistic road maps, and Markov models may be used to better understand protein dynamics and kinematics by discarding un- correlated, high-frequency atomic motions [112]. Elastic network models and normal mode analysis methods reveal collective motion and allosteric mechanisms in good agreement with NMR and X-ray scattering data [19], and often in conjunction with standard coarse-graining [202, 247, 378]. Methods such as transition path sampling, transition interface sampling, forward flux sampling, and weighted ensembles provide additional access to longer time-scales in atomistic systems [383]. In replica exchange molecular dynamics, multiple weakly-coupled simulations of the same system are exchanged between temperatures to escape kinetic traps [325]. Biasing potentials may be used to generate non-Boltzmann-distributed ensembles from which equilib- rium properties may be calculated in steered molecular dynamics [110]. Metadynam- ics [174], temperature-accelerated molecular dynamics [208], and other free energy perturbation methods [58, 73] and even Monte Carlo methods [155, 268, 376]. Perhaps the most thorough extension of atomistic molecular dynamics is realized by coupling simulation with NMR measurements, which enhance the sampling of the simulation at the longer time-scales possible in experiments [280, 377].
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Atomistic simulations to micro-mechanisms of adhesion in automotive applications

Atomistic simulations to micro-mechanisms of adhesion in automotive applications

The mechanical properties of DLC are particularly important since these films are generally used as a protective coating. DLC coatings have a high hardness and high elastic modulus, similar to diamond (which has a hardness of 100 GPa and elastic modulus of 1100 GPa), but with high internal stress. Most of the mechanical properties of DLC films were measured using nano-indentation experiments [70]. In these experiments, a small diamond tip is progressively forced into the film, and then force-displacement curve is obtained. Since DLC films are relatively harder materials, they show both a plastic and elastic response to indentation. Hardness is a measure of the resistance of a material to plastic deformation, defined as the average pressure under the indenter, and it is given by dividing the applied load by the projected area of plastic deformation, which is found by estimating the area in the loaded condition from the curve versus the indent depth. Young’s modulus is proportional to the slope of the tangent line that is drawn to the unloading curve at the maximum load, and extrapolated to zero load as described by the Oliver-Pharr method [71]. An accurate measurement of the mechanical properties for a hard film on a soft substrate system, such as DLC, can only be achieved when the indentation depth is limited to 10% of the thickness of the thin film [72].
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Atomistic Simulations of Formation of Elementary Zr I Systems

Atomistic Simulations of Formation of Elementary Zr I Systems

We report results of simulations on the formation of simple zirconium iodide molecules. Previous work by Wimmer et al. [1] explored the relationship between iodine and a zirconium surface. We investigate the re- action schemes through atomistic simulations to better understand the nature of Zr-I interactions through iso- lated molecules. The computed energy values of varying Zr-I systems suggests a strong binding mechanism between zirconium and iodine, and offer predictions of likely reaction products. The computed results pre- dict condensation of volatile ZrI 4 with ZrI 2 to form Zr 2 I 6 .
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Superelasticity of Carbon Nanocoils from Atomistic Quantum Simulations

Superelasticity of Carbon Nanocoils from Atomistic Quantum Simulations

With their unique three-dimensional (3D) helical struc- tures, the CNCs are expected to exhibit spring-like behavior in their mechanical properties. In an experiment by Chen et al. [24], multi-walled CNCs with outer tubular diameter of *126 nm have been elastically elongated to a maximum strain of *42%. A spring constant of 0.12 N/m in the low strain region was obtained. According to the structural parameters of nanocoil given by Chen et al. [24] (tubular diameter of 120 nm, coil radius of 420 nm, and pitch of 2,000 nm), Fonseca et al. [25] computed the CNC’s Young’s modulus within the framework of the Kirchhoff rod model and obtained a value of 6.88 GPa. Using finite element analysis at the continuum level, Sanada et al. also predicted a similar result (about 4.5 GPa) for carbon nanocoil with tubular radius of 240 nm, coil radius of 325 nm, and coil pitch of 1,080 nm [26]. How- ever, the experimentally measured Young’s modulus val- ues are much higher than these theoretical predictions. Volodin et al. [27] reported a Young’s modulus *0.7 TPa for CNCs with coil diameter [ 170 nm from AFM mea- surement. Using a manipulator-equipped SEM, Pan et al. determined the Young’s modulus of CNCs to be up to 0.1 TPa for coil diameter ranging from 144 to 830 nm [28]. The large discrepancy between experiment and theory has been attributed to the usage of mechanical parameters of bulk materials in the continuum mechanics simulations [25].
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Transaction taxes, traders’ behavior and exchange rate risks

Transaction taxes, traders’ behavior and exchange rate risks

Abstract: We propose a new model of chartist-fundamentalist-interaction in which both groups of traders are allowed to select endogenously between different forecasting models and different investment horizons. Stochastic interest rates in both countries and different behavioral assumptions for trend-extrapolating and fundamental based forecasts determine the agents’ market orders which drive the exchange rate. A numerical analysis of the model shows that it is able to replicate stylized facts of observed financial return time series like excess kurtosis and volatility clustering. Within this framework we study the effects of transaction taxes on exchange rate volatil- ity and traders’ behavior measured by their population fractions. Simula- tions yield the result that on the macroscopic level these taxes reduce the variance of exchange rate returns, but also increase their kurtosis. Moreover, on the microscopic level the tax harms short-term speculation in favor of long-term investment, while it also harms trading rules based on economic fundamentals in favor to trend extrapolating trading rules.
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Analysis of boundary conditions for crystal defect atomistic simulations

Analysis of boundary conditions for crystal defect atomistic simulations

These results are generally useful for the analysis of crystalline defects, how- ever, our own primary motivation was to provide a foundation for the analysis of atomistic multi-scale simulation methods, which in this context can be thought of as different means to produce boundary conditions for an atomistic defect core simulation. To demonstrate the applicability of our framework we analyzed sim- ple variants of some of the most commonly employed schemes: Dirichlet boundary conditions, periodic boundary conditions, far-field approximation via linearised lat- tice elasticity and via nonlinear continuum elasticity (Cauchy–Born, atomistic-to- continuum coupling). In parallel works [12,23,24,36] this framework has already been exploited resulting in new and improved formulations of atomistic/continuum and quantum/atomistic coupling schemes.
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Darwinian fisheries science needs to consider realistic fishing pressures over evolutionary time scales

Darwinian fisheries science needs to consider realistic fishing pressures over evolutionary time scales

ABSTRACT: The apparently intense selective differentials imposed by many fisheries may drive the rapid evolution of growth rates. In a widely-cited laboratory experiment, Conover & Munch (2002; Science 297:94–96) found considerable evolutionary change in the size of harvested fish over 4 gen- erations. Their empirical model has since been used to estimate the impact of fishery-driven evolu- tion on fishery sustainability. Using a mathematical, individual-based model (IBM) that simulates that experiment, we showed that the selection imposed in the Conover & Munch (2002) model is unreal- istically strong when compared to harvest rates in wild fisheries. We inferred the evolutionary change that could be expected over the timescale used by Conover & Munch (2002), had they simulated more realistic harvest regimes, and found that the magnitude in their original experiment was 2.5 to 5 times greater. However, over evolutionary timescales of 30 generations and with realistic fishing pressure, the results of Conover & Munch (2002) are comparable to wild fisheries. This simulation result pro- vides support for the use of empirical models to predict the impacts of fishery-driven evolution on yields and sustainability. Future models should consider the timing of fishing events, the trade-off between size, maturation and growth, and density-dependent effects for a comprehensive analysis of the consequences of fishery-driven evolution.
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Atomistic Simulations of Material Properties under Extreme Conditions

Atomistic Simulations of Material Properties under Extreme Conditions

The element carbon has received extensive attention for many centuries, not only because it is the backbone of biological molecules but because it is also one of the most abundant elements in the universe. Carbon is a primary constituent of white dwarfs and outer planets such as Uranus and Neptune [5] . Carbon has many practical and technological applications due to the remarkable and contrasting properties of its different allotropes, including the unique high-strength mechanical response of diamond (the only stable carbon phase under high-pressure experiments [6] ) versus the softness of graphite, or the low electrical conductivity of diamond versus the very good conductivity of graphite. The behavior and properties of carbon under extreme conditions are of great importance to understanding outer planet interiors, white dwarfs, and extra-solar carbon planets [7, 8] , as well as to tailoring new ablator materials capable of withstanding the operating conditions of, for example, inertial confinement fusion chambers [9] , or the hypervelocity reentry conditions of spatial vehicles.
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Atomistic molecular dynamics simulations of shock compressed quartz

Atomistic molecular dynamics simulations of shock compressed quartz

Before starting any MD simulations, it is essential to have a relaxed and stable system. Making a quartz slab by cleav- ing bulk quartz creates a large and unphysical dipole moment, which strongly effects the energetics of the system. Hence, the systems were first relaxed using a quasi-Newtonian optimi- sation algorithm along with the EW3DC which removed the dipole moment that was initially present. Figure 4 shows how the optimisation removed the dipole moment of the system after 50 steps and from there continued to relax the system to its final state. The final relaxed structure had negligible dipole moment across the slab.
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Towards Atomistic Materials Design (PSI-K)

Towards Atomistic Materials Design (PSI-K)

ESF Programme Towards Atomistic Materials Design (Psi-k). The underlying aim of all these activities was to unify Europe in our field and to make it the international leader. It is fair to say that to a large extent both objectives have been achieved. The two ESF Programmes have been vital in accomplishing this. The primary objective of the present Programme is to maintain and enhance the lead that Europe still holds by promoting research excellence and encouraging collaborations and the sharing of ideas, expertise and computer codes. Our field is currently in a state of strong growth and there are no signs that this will change in the foreseeable future. The Programme is structured around 15 topical working groups covering the whole field of ab initio calculations. The working groups as well as individual scientists make proposals for networking activities such as workshops and tutorials which have to be approved by the Steering Committee at its yearly meetings. Some of the working groups also participate in EU-funded research training networks or networks of excellence.
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Analysis of Reinforced Concrete Building under Blast Loading Using SAP 2000

Analysis of Reinforced Concrete Building under Blast Loading Using SAP 2000

For performing the linear and Non-linear analysis to the framed structure by manually, is very difficult task and also a time consuming process. So huge manual errors will occur when we done by manually. To eliminate this type of errors and recent few decades implemented some software’s to eliminate the difficulties. If we want to know the performance of any structure, firstly we should have to model the structure. So for modelling I opted for SAP2000. My intention is to determine the behaviour of the structure under blast loading. So to determine that first we should know the behaviour of explosion and shockwave then to model that building and to provide appropriate structural components. In order to accomplish the desire objectives, linear and nonlinear model time history analysis has been conducted on the building frames model in SAP2000 in this study. Concrete frame buildings have been taken where the frames have been used for performance evaluation and model using the background of software SAP2000. Using unified facilities criteria [1], the blast pressure time functions have been estimated and were applied to the building frames. Linear and nonlinear dynamic modal time history analysis is conducted for the modelled building frames. Subsequently analysis results were recorded for performance evaluation.
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Cerebral blood  flow simulations in realistic geometries

Cerebral blood flow simulations in realistic geometries

p q dx is usually added in FreeFem++ to obtain an invertible matrix (it is the so-called penalty method, see for details [4], Section 5.3.3). One of the key problem is the boundary conditions. For the inlet, we need to impose a periodic Poiseuille flow, which is a first approximation of the pulsatile flow going out from the heart. This condition is a Dirichlet one and is imposed strongly. For the outlet, there are several options. The simpler one, the so-called ”do nothing” condition is difficult to use with the symmetric formulation. As an example, we show the result of the bidimensional Poiseuille flow, where the solution is known : the velocity has a parabolic profile and the pressure is linear. We compare both solutions, one imposing on the outlet the same Poiseuille flow as on the inlet and one with the ”do nothing” condition. We can see on Figure 3 and Figure 4 that we obtain different solutions. For example, the pressure is no more linear with the ”do nothing” condition and what is imposed is only that the pressure is null at the middle of the outlet boundary (see [7] for similar results). Indeed, the ”do nothing” condition corresponds to impose the normal component of the stress tensor equal to zero and thus the flow is going out as a jet as physically expected. As we want to mimic the rest of the network (little arteries beyond the image resolution, veins and capillaries), which has to be cut in order to keep a reasonable simulation in terms of time and memory, we have to be aware that the ”do nothing” condition is not the appropriate one for our simulations. Indeed, the solution would be to couple the 3D simulation with a 1D model.
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Understanding Galaxy Formation and Evolution with Realistic Simulations

Understanding Galaxy Formation and Evolution with Realistic Simulations

Recent spatially resolved observations of galaxies at z ∼ 0 . 6–3 reveal that high- redshift galaxies show complex kinematics and a broad distribution of gas-phase metallicity gradients. To understand these results, we use a suite of high-resolution cosmological zoom-in simulations from the Feedback in Realistic Environments (FIRE) project, which include physically motivated models of the multi-phase ISM, star formation, and stellar feedback. Our simulations reproduce the observed di- versity of kinematic properties and metallicity gradients, broadly consistent with observations at z ∼ 0–3. Strong negative metallicity gradients only appear in galax- ies with a rotating disk, but not all rotationally supported galaxies have significant gradients. Strongly perturbed galaxies with little rotation always have flat gradients. The kinematic properties and metallicity gradient of a high-redshift galaxy can vary significantly on short time-scales, associated with starburst episodes. Feedback from a starburst can destroy the gas disk, drive strong outflows, and flatten a pre-existing negative metallicity gradient. The time variability of a single galaxy is statistically similar to the entire simulated sample, indicating that the observed metallicity gra- dients in high-redshift galaxies reflect the instantaneous state of the galaxy rather than the accretion and growth history on cosmological time-scales. We find weak dependence of metallicity gradient on stellar mass and specific star formation rate (sSFR). Low-mass galaxies and galaxies with high sSFR tend to have flat gradients, likely due to the fact that feedback is more efficient in these galaxies. We argue that it is important to resolve feedback on small scales in order to produce the diverse metallicity gradients observed.
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Mapping continuous potentials to discrete forms

Mapping continuous potentials to discrete forms

Overall, setting the step energy through a volume average of the energy of the underlying continuous potential appears to yield a good approximation, provided Θ > 1. The additional complexity of a temperature-dependent potential through using the Virial approach does not appear justified at these conditions unless Θ < 1, but the reproduction of the internal energy is unacceptable at such a low order of approximation. Although it might be expected that the temperature dependence will become increasingly important at lower temperatures, further simulations carried out in the liquid branch at k B T /ε = 0.85 and ρσ 3 = 0.85 yielded similar
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Dislocation Driven Problems in Atomistic Modelling of Materials

Dislocation Driven Problems in Atomistic Modelling of Materials

Body-centred cubic (bcc) transition metals and their alloys, including a wide range of ferritic/matersitic steels, have recently been identified as prime candidates for future fusion power plants, because they do not react readily with neutrons under irradiation, undergo limited swelling and helium embrittlement, and can be used with a range of possible coolants. Experiment shows that screw dislocations in bcc metals are less mobile than edge dislocations below a certain temperature, and applied stress causes mobile dislocations to be eliminated, leaving screw dislocations to control the plastic behavior. To understand the dynamics of dislocations in atomistic detail at finite temperature and under stress it is necessary to perform molecular dynamics simulations in which an accurate description of inter-atomic forces between atoms is crucial. Within the TBB based bond-
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NemoViz: a visual interactive system for atomistic simulations design

NemoViz: a visual interactive system for atomistic simulations design

Toolkits have been proposed to implement the sim- ple two-layer graphical interface. (McLennan and Kennell 2010) and nanoHUB (Lundstrom and Klimeck 2006) pro- vide a XML API that enables the graphical interface. Rappture allows users to not only describe the simu- lation models and visualize the simulation results, but also to execute experiments during the technical phase. For example, the Quantum Dot lab (Klimeck et al. 2006) employs NEMO5 to calculate electrical and optical prop- erties of quantum dots; therefore, users can run exper- iments on different qdot sizes and materials. This tool presents the first layer of graphical control elements to set the simulation parameters. Then the results are dis- played in a second layer that includes visualizations of the electron wave functions and optical properties. A limited number of visualizations are supported by Rappture, and additional visualizations require significant developments of the Rappture infrastructure (Zhao et al. 2017).
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Structure and properties of nanostructured materials from atomistic modeling and advanced diffraction methods

Structure and properties of nanostructured materials from atomistic modeling and advanced diffraction methods

In the above equation, the self-correlation func- tion (Ω) represents the part of the intensity scattered by atoms inside grain p when considered as an isolated object (ω p ), whereas th[r]

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

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

In simulations at room temperature (300 K), six water molecules bond to the Al clusters. Formation of these Al- O bonds enhances the Lewis-base character of Al atoms that are not connected to the water molecules, thereby preventing further bonding of water molecules to the Al clusters. Dissociation of water molecules is not observed within the limited simulation time (several ps) at this temperature. Even when the temperature is raised to 500 K, still no water molecule dissociates. The atomistic process of hydrogen production is successfully observed at 1000 K. In total, three hydrogen molecules are produced within 6 ps.
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