Publications

Thompson, Aidan P.

Abstract not provided.

Thompson, Aidan P.

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Crozier, Paul C.; Plimpton, Steven J.; Thompson, Aidan P.

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Journal of Computational Chemistry

Slepoy, Alexander S.; Peters, Michael D.; Thompson, Aidan P.

Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. © 2007 Wiley Periodicals, Inc.

Thompson, Aidan P.

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Thompson, Aidan P.

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Thompson, Aidan P.

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Alexander, Charles S.; Thompson, Aidan P.; Chhabildas, Lalit C.; Furnish, Michael D.; Dolan, Daniel H.; Davis, Jean-Paul D.; Lemke, Raymond W.; Desjarlais, Michael P.; Hertel, Eugene S.

Abstract not provided.

Lo, Chi S.; Thompson, Aidan P.; Grest, Gary S.

Using molecular dynamics simulations, a constitutive model for the chemical aging of polymer networks was developed. This model incorporates the effects on the stress from the chemical crosslinks and the physical entanglements. The independent network hypothesis has been modified to account for the stress transfer between networks due to crosslinking and scission in strained states. This model was implemented in the finite element code Adagio and validated through comparison with experiment. Stress relaxation data was used to deduce crosslinking history and the resulting history was used to predict permanent set. The permanent set predictions agree quantitatively with experiment.

Thompson, Aidan P.

Abstract not provided.

Budzien, Joanne L.; Lo, Chi S.; Grest, Gary S.; Thompson, Aidan P.

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Lo, Chi S.; Thompson, Aidan P.

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Physical Review B - Condensed Matter and Materials Physics

Edwards, Arthur H.; Pineda, Andrew C.; Schultz, Peter A.; Martin, Marcus G.; Thompson, Aidan P.; Hjalmarson, Harold P.; Umrigar, Cyrus J.

Germanium telluride undergoes rapid transition between polycrystalline and amorphous states under either optical or electrical excitation. While the crystalline phases are predicted to be semiconductors, polycrystalline germanium telluride always exhibits p -type metallic conductivity. We present a study of the electronic structure and formation energies of the vacancy and antisite defects in both known crystalline phases. We show that these intrinsic defects determine the nature of free-carrier transport in crystalline germanium telluride. Germanium vacancies require roughly one-third the energy of the other three defects to form, making this by far the most favorable intrinsic defect. While the tellurium antisite and vacancy induce gap states, the germanium counterparts do not. A simple counting argument, reinforced by integration over the density of states, predicts that the germanium vacancy leads to empty states at the top of the valence band, thus giving a complete explanation of the observed p -type metallic conduction.

Curro, John G.; Budzien, Joanne L.; Grest, Gary S.; Thompson, Aidan P.

The Independent Network Model (INM) has proven to be a useful tool for understanding the development of permanent set in strained elastomers. Our previous work showed the applicability of the INM to our simulations of polymer systems crosslinking in strained states. This study looks at the INM applied to theoretical models incorporating entanglement effects, including Flory's constrained junction model and more recent tube models. The effect of entanglements has been treated as a separate network formed at gelation, with additional curing treated as traditional phantom contributions. Theoretical predictions are compared with large-scale molecular dynamics simulations.

Budzien, Joanne L.; Lo, Chi S.; Curro, John G.; Thompson, Aidan P.; Grest, Gary S.

Constitutive models for chemically reacting networks are formulated based on a generalization of the independent network hypothesis. These models account for the coupling between chemical reaction and strain histories, and have been tested by comparison with microscopic molecular dynamics simulations. An essential feature of these models is the introduction of stress transfer functions that describe the interdependence between crosslinks formed and broken at various strains. Efforts are underway to implement these constitutive models into the finite element code Adagio. Preliminary results are shown that illustrate the effects of changing crosslinking and scission rates and history.

Thompson, Aidan P.

We performed molecular dynamics simulations of beta-amyloid (A{beta}) protein and A{beta} fragment(31-42) in bulk water and near hydrated lipids to study the mechanism of neurotoxicity associated with the aggregation of the protein. We constructed full atomistic models using Cerius2 and ran simulations using LAMMPS. MD simulations with different conformations and positions of the protein fragment were performed. Thermodynamic properties were compared with previous literature and the results were analyzed. Longer simulations and data analyses based on the free energy profiles along the distance between the protein and the interface are ongoing.

Thompson, Aidan P.

Abstract not provided.

Thompson, Aidan P.; Slepoy, Alexander S.; Davidson, George S.; Peters, Michael D.

Abstract not provided.

Thompson, Aidan P.

The goal of this Laboratory Directed Research & Development (LDRD) effort was to design, synthesize, and evaluate organic-inorganic nanocomposite membranes for solubility-based separations, such as the removal of higher hydrocarbons from air streams, using experiment and theory. We synthesized membranes by depositing alkylchlorosilanes on the nanoporous surfaces of alumina substrates, using techniques from the self-assembled monolayer literature to control the microstructure. We measured the permeability of these membranes to different gas species, in order to evaluate their performance in solubility-based separations. Membrane design goals were met by manipulating the pore size, alkyl group size, and alkyl surface density. We employed molecular dynamics simulation to gain further understanding of the relationship between membrane microstructure and separation performance.

Proposed for publication in the Journal of Chemical Physics.

Thompson, Aidan P.; Thompson, Aidan P.

Abstract not provided.

Thompson, Aidan P.; Thompson, Aidan P.

In the LIGA process for manufacturing microcomponents, a polymer film is exposed to an x-ray beam passed through a gold pattern. This is followed by the development stage, in which a selective solvent is used to remove the exposed polymer, reproducing the gold pattern in the polymer film. Development is essentially polymer dissolution, a physical process which is not well understood. We have used coarse-grained molecular dynamics simulation to study the early stage of polymer dissolution. In each simulation a film of non-glassy polymer was brought into contact with a layer of solvent. The mutual penetration of the two phases was tracked as a function of time. Several film thicknesses and two different chain lengths were simulated. In all cases, the penetration process conformed to ideal Fickian diffusion. We did not see the formation of a gel layer or other non-ideal effects. Variations in the Fickian diffusivities appeared to be caused primarily by differences in the bulk polymer film density.

Thompson, Aidan P.

The final report for a Laboratory Directed Research and Development project entitled, Molecular Simulation of Reacting Systems is presented. It describes efforts to incorporate chemical reaction events into the LAMMPS massively parallel molecular dynamics code. This was accomplished using a scheme in which several classes of reactions are allowed to occur in a probabilistic fashion at specified times during the MD simulation. Three classes of reaction were implemented: addition, chain transfer and scission. A fully parallel implementation was achieved using a checkerboarding scheme, which avoids conflicts due to reactions occurring on neighboring processors. The observed chemical evolution is independent of the number of processors used. The code was applied to two test applications: irreversible linear polymerization and thermal degradation chemistry.

Journal of Physical Chemistry B

Chandross, M.; Webb, Edmund B.; Grest, Gary S.; Martin, Marcus G.; Thompson, Aidan P.; Roth, M.W.

We present the results of Molecular Dynamics and Monte Carlo simulations of n-butane and isobutane in silicalite. We begin with a comparison of the bulk adsorption and diffusion properties for two different parameterizations of the interaction potential between the hydrocarbon species, both of which have been shown to reproduce experimental gas-liquid coexistence curves. We examine diffusion as a function of the loading of the zeolite, as well as the temperature dependence of the diffusion constant at loading and for infinite dilution. Both force fields give accurate descriptions of bulk properties. We continue with simulations in which interfaces are formed between single component gases and the zeolite. After reaching equilibrium, we examine the dynamics of exchange between the bulk gas and the zeolite. In particular, we examine the average time spent in the adsorption layer by molecules as they enter the zeolite from the gas in an attempt to probe the microscopic origins of the surface barrier. The microscopic barrier is found to be insignificant for experimental systems. Finally, we calculate the permeability of the zeolite for n-butane and isobutane as a function of pressure. Our results underestimate the experimental results by an order of magnitude, indicating a strong effect from the surface barrier in these simulations. Our simulations are performed for a number of different gas temperatures and pressures, covering a wide range of state points.

Journal of Chemical Physics

Martin, Marcus G.; Thompson, Aidan P.; Nenoff, T.M.

Abstract not provided.

Fang, H.E.; Miller, Samuel L.; Dugger, Michael T.; Prasad, Somuri V.; Reedy, Earl D.; Thompson, Aidan P.; Wong, Chungnin C.; Yang, Pin Y.; Battaile, Corbett C.; Battaile, Corbett C.; Benavides, Gilbert L.; Ensz, M.T.; Buchheit, Thomas E.; Chen, Er-Ping C.; Christenson, Todd R.; De Boer, Maarten P.

This report summarizes materials issues associated with advanced micromachines development at Sandia. The intent of this report is to provide a perspective on the scope of the issues and suggest future technical directions, with a focus on computational materials science. Materials issues in surface micromachining (SMM), Lithographic-Galvanoformung-Abformung (LIGA: lithography, electrodeposition, and molding), and meso-machining technologies were identified. Each individual issue was assessed in four categories: degree of basic understanding; amount of existing experimental data capability of existing models; and, based on the perspective of component developers, the importance of the issue to be resolved. Three broad requirements for micromachines emerged from this process. They are: (1) tribological behavior, including stiction, friction, wear, and the use of surface treatments to control these, (2) mechanical behavior at microscale, including elasticity, plasticity, and the effect of microstructural features on mechanical strength, and (3) degradation of tribological and mechanical properties in normal (including aging), abnormal and hostile environments. Resolving all the identified critical issues requires a significant cooperative and complementary effort between computational and experimental programs. The breadth of this work is greater than any single program is likely to support. This report should serve as a guide to plan micromachines development at Sandia.