High performance computing for the application of molecular theories to biological systems
Abstract not provided.
Abstract not provided.
Physical Review B - Condensed Matter and Materials Physics
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.
Proposed for publication in the Proceedings of the National Academy of Sciences.
Abstract not provided.
This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.
Journal of Chemical Physics
Dual control volume molecular dynamics was employed to study the flux of methane through channels of thin silicalite membranes. The DCANIS force field was analyzed to describe the adsorption isotherms of methane and ethane in silicalite. The alkane parameters and silicalite parameters were determined by fiiting the DCANIS force field to single-component vapor-liquid coexistence curves (VLCC) and adsorption isotherms respectively. The adsorption layers on the surfaces of thin silicalite membranes showed a sifnificant resistance to the flux of methane. The results depicted the insensitivity of permeance to both the average pressure and pressure drop.
Jornal of Physical Chemistry B
The authors present the results of molecular dynamics simulations of n-butane and isobutane in silicalite. They 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. They 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. They continue with simulations in which interfaces are formed between single component gases and the zeolite. After reaching equilibrium, they examine the dynamics of exchange between the bulk gas and the zeolite. Finally, they calculate the permeability of the zeolite for n-butane and isobutane as a function of pressure. Their simulations are performed for a number of different gas temperatures and pressures, covering a wide range of state points.