Biomedical subjects

Gregory Grochola

Publications and source records attributed to Gregory Grochola.

4 recordsLinked to original sources

PubMed2005

Application of the constrained fluid lambda-integration path to the calculation of high temperature Au(110) surface free energies.

Recently a method termed constrained fluid lambda-integration was proposed for calculating the free energy difference between bulk solid and liquid reference states via the construction of a reversible thermodynamic integration path; coupling the two states in question. The present work shows how the application of the constrained fluid lambda-integration concept to solid/liquid slab simulation cells makes possible a generally applicable computer simulation methodology for calculating the free energy of any surface and/or surface defect structure, including surfaces requiring variations in surface atom or density number, such as the (1 x 5) Au(100) or (1 x 2) missing row Au(110) reconstructed surfaces or excess adatom/vacancy/step populated surfaces. We evaluate the methodology by calculating the free energy of various disordered high temperature Au(110) embedded atom method surfaces constrained to differing excess surface atom numbers [including those corresponding to the (1 x 2) missing row reconstructed surface] and obtained the interesting result that at 1000 K (as distinct from lower temperatures) the free energy difference between these surfaces is reduced to zero; a result which is consistent with an expected order-disorder phase transition for the Au(110) surface at such high temperatures.

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PubMed2005

Further application of the constrained fluid lambda-integration method.

Previously we proposed a three stage, and recently a single stage nonphysical lambda-integration path for thermodynamically coupling bulk solid and liquid states directly. In this work we further apply these paths, specifically the newer single stage path, to the calculation of the complete truncated and shifted Lennard-Jones (R(cutoff)=2.5sigma) and aluminum glue potential melting lines, and the zero pressure melting point for a commonly used gold glue potential. The results showed accurate agreement with presently available literature. We found the single stage constrained fluid lambda-integration methodology to be robust in terms of reversibility over this extended range of temperatures, pressures, and intermolecular potentials.

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PubMed2004

"Exact" surface free energies of iron surfaces using a modified embedded atom method potential and lambda integration.

Previously a new universal lambda-integration path and associated methodology was developed for the calculation of "exact" surface and interfacial free energies of solids. Such a method is in principle applicable to any intermolecular potential function, including those based on ab initio methods, but in previous work the method was only tested using a relatively simple embedded atom method iron potential. In this present work we apply the new methodology to the more sophisticated and more accurate modified embedded atom method (MEAM) iron potential, where application of other free- energy methods would be extremely difficult due to the complex many-body nature of the potential. We demonstrate that the new technique simplifies the process of obtaining "exact" surface free energies by calculating the complete set of these properties for the low index surface faces of bcc and fcc solid iron structures. By combining these data with further calculations of liquid surface tensions we obtain the first complete set of exact surface free energies for the solid and liquid phases of a realistic MEAM model system. We compare these predictions to various experimental and theoretical results.

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PubMed2004

Constrained fluid lambda-integration: constructing a reversible thermodynamic path between the solid and liquid state.

A novel lambda-integration path is proposed for calculating the Gibbs free energy difference between any arbitrary solid and liquid state needed for the location of melting lines. This technique involves reversibly forcing a liquid state to a solid state across the phase transition along a nonphysical path, thermodynamically coupling the two states directly. The process eliminates the need for coupling to idealized reference states as is presently performed and hence simplifies the location of phase transitions for computer simulation systems. More specifically the path involves a three stage process, whereby, initially a liquid state is transformed to a weakly attractive fluid using linear lambda-integration scaling of the intermolecular potential. In the second stage, the resulting fluid is then constrained to the required solid configurational phase space via the insertion of a periodic lattice of 3D Gaussian wells. The final stage involves reversing to full strength the main intermolecular potential while gradually turning off the constraining 3D Gaussian lattice finally resulting in a stable (or metastable) solid state. Each stage was found to be completely reversible and the resulting change in free energy was thermodynamically integrable. The methodology is demonstrated and validated by calculating solid-liquid coexistence points using the new technique and comparing to those in present literature for the truncated and shifted Lennard-Jones system. The results are found to be in good agreement. The new method is not limited to melting phase transitions and is readily applicable to any simulation methodology, simulation cell size and/or intermolecular potential including ab initio methods.

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