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Comparison of molecular dynamics with classical density functional and Poisson-Boltzmann theories of the electric double layer in nanochannels

Journal of Chemical Theory and Computation

Lee, Jonathan W.; Nilson, Robert H.; Templeton, Jeremy A.; Griffiths, Stewart K.; Kung, Andy K.; Wong, Bryan M.

Comparisons are made among Molecular Dynamics (MD), Classical Density Functional Theory (c-DFT), and Poisson-Boltzmann (PB) modeling of the electric double layer (EDL) for the nonprimitive three component model (3CM) in which the two ion species and solvent molecules are all of finite size. Unlike previous comparisons between c-DFT and Monte Carlo (MC), the present 3CM incorporates Lennard-Jones interactions rather than hard-sphere and hard-wall repulsions. c-DFT and MD results are compared over normalized surface charges ranging from 0.2 to 1.75 and bulk ion concentrations from 10 mM to 1 M. Agreement between the two, assessed by electric surface potential and ion density profiles, is found to be quite good. Wall potentials predicted by PB begin to depart significantly from c-DFT and MD for charge densities exceeding 0.3. Successive layers are observed to charge in a sequential manner such that the solvent becomes fully excluded from each layer before the onset of the next layer. Ultimately, this layer filling phenomenon results in fluid structures, Debye lengths, and electric surface potentials vastly different from the classical PB predictions. © 2012 American Chemical Society.

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Experiences using DAKOTA stochastic expansion methods in computational simulations

Ruthruff, Joseph R.; Templeton, Jeremy A.

Uncertainty quantification (UQ) methods bring rigorous statistical connections to the analysis of computational and experiment data, and provide a basis for probabilistically assessing margins associated with safety and reliability. The DAKOTA toolkit developed at Sandia National Laboratories implements a number of UQ methods, which are being increasingly adopted by modeling and simulation teams to facilitate these analyses. This report disseminates results as to the performance of DAKOTA's stochastic expansion methods for UQ on a representative application. Our results provide a number of insights that may be of interest to future users of these methods, including the behavior of the methods in estimating responses at varying probability levels, and the expansion levels for the methodologies that may be needed to achieve convergence.

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Atom-to-continuum methods for gaining a fundamental understanding of fracture

Jones, Reese E.; Zimmerman, Jonathan A.; Templeton, Jeremy A.; Zhou, Xiaowang Z.; Moody, Neville R.; Reedy, Earl D.

This report describes an Engineering Sciences Research Foundation (ESRF) project to characterize and understand fracture processes via molecular dynamics modeling and atom-to-continuum methods. Under this aegis we developed new theory and a number of novel techniques to describe the fracture process at the atomic scale. These developments ranged from a material-frame connection between molecular dynamics and continuum mechanics to an atomic level J integral. Each of the developments build upon each other and culminated in a cohesive zone model derived from atomic information and verified at the continuum scale. This report describes an Engineering Sciences Research Foundation (ESRF) project to characterize and understand fracture processes via molecular dynamics modeling and atom-to-continuum methods. The effort is predicated on the idea that processes and information at the atomic level are missing in engineering scale simulations of fracture, and, moreover, are necessary for these simulations to be predictive. In this project we developed considerable new theory and a number of novel techniques in order to describe the fracture process at the atomic scale. Chapter 2 gives a detailed account of the material-frame connection between molecular dynamics and continuum mechanics we constructed in order to best use atomic information from solid systems. With this framework, in Chapter 3, we were able to make a direct and elegant extension of the classical J down to simulations on the scale of nanometers with a discrete atomic lattice. The technique was applied to cracks and dislocations with equal success and displayed high fidelity with expectations from continuum theory. Then, as a prelude to extension of the atomic J to finite temperatures, we explored the quasi-harmonic models as efficient and accurate surrogates of atomic lattices undergoing thermo-elastic processes (Chapter 4). With this in hand, in Chapter 5 we provide evidence that, by using the appropriate energy potential, the atomic J integral we developed is calculable and accurate at finite/room temperatures. In Chapter 6, we return in part to the fundamental efforts to connect material behavior at the atomic scale to that of the continuum. In this chapter, we devise theory that predicts the onset of instability characteristic of fracture/failure via atomic simulation. In Chapters 7 and 8, we describe the culmination of the project in connecting atomic information to continuum modeling. In these chapters we show that cohesive zone models are: (a) derivable from molecular dynamics in a robust and systematic way, and (b) when used in the more efficient continuum-level finite element technique provide results that are comparable and well-correlated with the behavior at the atomic-scale. Moreover, we show that use of these same cohesive zone elements is feasible at scales very much larger than that of the lattice. Finally, in Chapter 9 we describe our work in developing the efficient non-reflecting boundary conditions necessary to perform transient fracture and shock simulation with molecular dynamics.

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Coupled ionic and electronic heat transport at the nanoscale

Modine, N.A.; Jones, Reese E.; Templeton, Jeremy A.

In modeling thermal transport in nanoscale systems, classical molecular dynamics (MD) explicitly represents phonon modes and scattering mechanisms, but electrons and their role in energy transport are missing. Furthermore, the assumption of local equilibrium between ions and electrons often fails at the nanoscale. We have coupled MD (implemented in the LAMMPS MD package) with a partial differential equation based representation of the electrons (implemented using finite elements). The coupling between the subsystems occurs via a local version of the two-temperature model. Key parameters of the model are calculated using the Time Dependent Density Functional Theory with either explicit or implicit energy flow. We will discuss application of this work in the context of the US DOE Center for Integrated Nanotechnologies (CINT).

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A long-range electric field solver for molecular dynamics of fluid-solid interfaces based on atomistic-to-continuum modeling

Templeton, Jeremy A.; Jones, Reese E.; Zimmerman, Jonathan A.; Wong, Bryan M.

Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anisotropic electric fields, as occur at charged fluid/solid interfaces, in molecular dynamics (MD) simulations. In this work, we develop a model for including electric fields in MD using an atomistic-to-continuum framework. Our model represents the electric potential on a finite element mesh satisfying a Poisson equation with source terms determined by the distribution of the atomic charges. The method is verified using simulations where analytical solutions are known or comparisons can be made to existing techniques. A Calculation of a salt water solution in a silicon nanochannel is performed to demonstrate the method in a target scientific application.

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Coupled thermomechanical modeling using dissimilar geometries in arpeggio

Kostka, Timothy D.; Templeton, Jeremy A.

Performing coupled thermomechanical simulations is becoming an increasingly important aspect of nuclear weapon (NW) safety assessments in abnormal thermal environments. While such capabilities exist in SIERRA, they have thus far been used only in a limited sense to investigate NW safety themes. An important limiting factor is the difficulty associated with developing geometries and meshes appropriate for both thermal and mechanical finite element models, which has limited thermomechanical analysis to simplified configurations. This work addresses the issue of how to perform coupled analyses on models where the underlying geometries and associated meshes are different and tailored to their relevant physics. Such an approach will reduce the model building effort and enable previously developed single-physics models to be leveraged in future coupled simulations. A combined-environment approach is presented in this report using SIERRA tools, with quantitative comparisons made between different options in SIERRA. This report summarizes efforts on running a coupled thermomechanical analysis using the SIERRA Arpeggio code.

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A material frame approach for evaluating continuum variables in atomistic simulations

Journal of Computational Physics

Zimmerman, Jonathan A.; Jones, Reese E.; Templeton, Jeremy A.

We present a material frame formulation analogous to the spatial frame formulation developed by Hardy, whereby expressions for continuum mechanical variables such as stress and heat flux are derived from atomic-scale quantities intrinsic to molecular simulation. This formulation is ideally suited for developing an atomistic-to-continuum correspondence for solid mechanics problems. We derive expressions for the first Piola-Kirchhoff (P-K) stress tensor and the material frame heat flux vector directly from the momentum and energy balances using localization functions in a reference configuration. The resulting P-K stress tensor, unlike the Cauchy expression, has no explicit kinetic contribution. The referential heat flux vector likewise lacks the kinetic contribution appearing in its spatial frame counterpart. Using a proof for a special case and molecular dynamics simulations, we show that our P-K stress expression nonetheless represents a full measure of stress that is consistent with both the system virial and the Cauchy stress expression developed by Hardy. We also present an expanded formulation to define continuum variables from micromorphic continuum theory, which is suitable for the analysis of materials represented by directional bonding at the atomic scale. © 2009 Elsevier Inc.

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Development of Advanced Continuum Models that Incorporate Nanomechanical Deformation into Engineering Analysis

Zimmerman, Jonathan A.; Jones, Reese E.; Templeton, Jeremy A.

Materials with characteristic structures at nanoscale sizes exhibit significantly different mechanical responses from those predicted by conventional, macroscopic continuum theory. For example, nanocrystalline metals display an inverse Hall-Petch effect whereby the strength of the material decreases with decreasing grain size. The origin of this effect is believed to be a change in deformation mechanisms from dislocation motion across grains and pileup at grain boundaries at microscopic grain sizes to rotation of grains and deformation within grain boundary interface regions for nanostructured materials. These rotational defects are represented by the mathematical concept of disclinations. The ability to capture these effects within continuum theory, thereby connecting nanoscale materials phenomena and macroscale behavior, has eluded the research community. The goal of our project was to develop a consistent theory to model both the evolution of disclinations and their kinetics. Additionally, we sought to develop approaches to extract continuum mechanical information from nanoscale structure to verify any developed continuum theory that includes dislocation and disclination behavior. These approaches yield engineering-scale ex-pressions to quantify elastic and inelastic deformation in all varieties of materials, even those that possess highly directional bonding within their molecular structures such as liquid crystals, covalent ceramics, polymers and biological materials. This level of accuracy is critical for engineering design and thermo-mechanical analysis is performed in micro- and nano systems. The research proposed here innovates on how these nanoscale deformation mechanisms should be incorporated into a continuum mechanical formulation, and provides the foundation upon which to develop a means for predicting the performance of advanced engineering materials.

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A mathematical framework for multiscale science and engineering : the variational multiscale method and interscale transfer operators

Bochev, Pavel B.; Collis, Samuel S.; Jones, Reese E.; Lehoucq, Richard B.; Parks, Michael L.; Scovazzi, Guglielmo S.; Silling, Stewart A.; Templeton, Jeremy A.; Wagner, Gregory J.

This report is a collection of documents written as part of the Laboratory Directed Research and Development (LDRD) project A Mathematical Framework for Multiscale Science and Engineering: The Variational Multiscale Method and Interscale Transfer Operators. We present developments in two categories of multiscale mathematics and analysis. The first, continuum-to-continuum (CtC) multiscale, includes problems that allow application of the same continuum model at all scales with the primary barrier to simulation being computing resources. The second, atomistic-to-continuum (AtC) multiscale, represents applications where detailed physics at the atomistic or molecular level must be simulated to resolve the small scales, but the effect on and coupling to the continuum level is frequently unclear.

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Results 76–96 of 96
Results 76–96 of 96