In This Issue: Supernova Remnants Upcoming Symposia People & Visitors Obituary Seminar Synopses Research Reports

[Research Bulletins] [Supercomputer Institute Homepage]







Structure-Preserving Integrators for Hamiltonian and Mechanical Systems
Laurent Jay
Computer Science, University of Minnesota

This seminar was concerned with the numerical solution of Hamiltonian and mechanical systems with holonomic constraints. Such problems arise, for example, in multibody dynamics. A class of methods was presented based on Lobatto points which preserve (or quasi-preserve) certain features of the flow: symplecticity, reversibility, the manifold of constraints, momentum, and energy. Conservative mechanical systems do not even need to be rewritten in Hamiltonian form to preserve these invariants. The Coriolis forces even cancel out in the new formulation. The proposed methods are superconvergent and they possess good stability properties: L-stability, P-stability, and unconditional explosivity. Structure-preserving methods are of interest for the long-time integration. Some issues related to a reversible variable-stepsize implementation were briefly discussed.

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Langevin Dynamics Simulations of a New Simplified Model of Protein Folding
Germana Paterlini
Medicinal Chemistry Department, University of Minnesota

The de novo prediction of the native structure of proteins by all-atom models is encumbered by the large number of variables in the system and by the complexity of the resulting energy landscape. One approach to solve the protein folding problem has been to create simplified models which use a reduced representation of the protein's geometry and energetics. A key element for the success of simplified models is the ability to capture the nature of both short and long range interaction energies and the interplay between them. Furthermore, an accurate representation of the geometry of the polypeptide backbone is crucial, if any comparisons to actual all-atom native protein structures are to be made. In this seminar, a simplified model was presented.

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The Chemodynamics of Superbubbles in Dwarf Galaxies
Robert Benjamin
Astronomy Department
University of Minnesota

The ejection of interstellar gas due to the energy input from supernovae is fundamentally associated with the life history of a galaxy. These mass flows are indicators of supernova and star formation activity in a galaxy and drive mass flows that affect chemical evolution. This speaker presented the results of two-dimensional hydrodynamical simulations designed to study the chemical and dynamical evolution of dwarf irregular galaxies. He examined the effects of the energy and mass injection of supernovae and followed the evolution of the resultant "superbubble" of hot interstellar gas. Benjamin discussed two unique features of the code; namely, the ability to track the cosmic chemical abundances as a function of time and position in a galaxy, and the inclusion of radiative cooling in the interstellar plasma.

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Numerical Modeling of Folds and Other Structures in Layered Rocks
Labao Lan
Geology & Geophysics Department
University of Minnesota

Laboratory studies indicate that most rocks behave as fluids under slow natural deformation, and that linear flow is expected for diffusion-controlled deformation and non-linear flow is expected for crystal- plastic deformation. The contrast in rheological properties between rock layers give rise to perturbations in flow resulting in geological structures such as folds, boudinage, inverse folds and mullions. Folds, the most common of these structures, result from deformation involving layer-parallel compressive stresses. This talk focused on the role of non-linearity of viscosity in the development of folds in isolated single layers. The supercomputer research has employed a two-dimensional finite element model of incompressible flow in power-law viscous fluids to investigate how fold shape and associated strain pattern vary as a function of the power-law exponent of the stiffer layers.

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Elaborate Microstructures Produced By Diblock Copolymers
Mark Matsen
Chemical Engineering
University of Minneosta

Diblock copolymer molecules are linear polymers with two chemically distinct portions-the usually immiscible A and B blocks. Without the chemical bond joining them, the blocks would phase separate. But, because they are connected, the A and B blocks can only separate on the microscopic scale. The resulting microphase separation produces a periodic ordered structure. which can assume numerous geometries, depending on the relative size of the two blocks. This speaker discussed an experimental phase diagram and described the complicated geometries involved. A simple model was introduced that included all the relevant details of a diblock copolymer melt and some simple "back of the envelope" calculations explained the physics in such a system. To conclude he presented the results of more advanced mean-field treatment, which have produced remarkable agreement with experiment.

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Rayleigh-Taylor Instability in Young Supernova Remnants
Byung-Il Jun
Astronomy Department
University of Minnesota

Supernova remnants are the relic of the vigorous explosion of stars in the late stage of their evolution. Young supernova remnants (age of a few hundred years) generally show very bright circular clumpy shell in radio emission. The magnetic field strength in the radio shell has been inferred to be in the range of 10^-4 to 10^-3 Gauss which is much higher than the field strength in the interstellar medium (10^-6). The interface between the star material and the interstellar material is known to be Rayleigh-Taylor unstable. This speaker has modeled the Rayleigh-Taylor instability to explain the origin of strong magnetic field in young supernova remnants. He talked first about the results of three-dimensional magnetohydrodynamic simulations of classical Rayleigh-Taylor instability. Secondly, the speaker presented the results of more realistic modeling of Rayleigh-Taylor instability in supernova remnants by using a moving grid technique in three-dimensional space.

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Molecular Dynamics Study of the Metal-Liquid Interface
Yu Zhou
Physics & Astronomy Department
University of Minnesota

Quantitative, predictive theories for metal-electrolyte interfaces require an atomic-scale representation of the interface and a description of the electronic density and structure. Such a complex system presents a difficult computational problem which has historically been tackled in pieces. A complete and self-consistent determination of the surface structure would involve a simultaneous calculation of both the atomic and electronic structure of the interface. This seminar included a discussion of a Car-Parrinello type combination of molecular dynamics and density functional methods in simulations of metal-electrolyte interface. The research discussed involved investigation of chlorine ion adsorption on the copper surface in contact with water. This was investigated to better understand the strong catalysis of electrode reactions by Cl ions that have been observed experimentally. This study will allow analysis of the charge-transfer process at the interface, which is of great importance to such technological subjects as batteries, fuel cells and corrosion.

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Polarizable Continuum Model: Recent Developments and Applications
Laura Coitiño
Chemistry Department
University of Minnesota

Most processes of interest in biochemistry and industry take place in solution. A proper understanding of the complex nature of chemical reactivity in the presence of solvent is the ultimate goal of theoretical chemistry in this area. The Polarizable Continuum Model (PCM) developed at the University of Pisa has become recognized for accurate studies on small solutes (ab initio evaluation of properties, both at the Hartree-Fock and correlated levels, detailed description of reaction mechanisms, etc.). Large or very large molecular solutes can also be treated by PCM using a simpler description of the solute charge distribution (semiempirical, semiclassical) with the loss of some accuracy. In recent years this speaker has devoted her efforts to developing more efficient and complete versions of the model that enable extension of the field of application of PCM to larger systems. A description of the most recent developments and their performance was given in this seminar.

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