posted on November 11, 2013 recently published a story about children with a rare skin disorder, epidermolysis bullosa (EB). People affected with this condition have very fragile skin that blisters or breaks easily. EB is painful, disfiguring, and can cause a shorted lifespan. It is a result of genetic mutations that block the body’s ability to make collagen, which is responsible for holding the layers of the skin together.

MSI Principal Investigator Jakub Tolar, Director of the Stem Cell Institute and an associate professor in the pediatrics department of the University of Minnesota Medical School, is quoted in the story. Professor Tolar uses MSI resources for his research into EB, especially the mechanisms of the pain and itching associated with it.


posted on November 7, 2013

Professor John Gulliver (Civil Engineering, St. Anthony Falls Laboratory, and Institute on the Environment Resident Fellow) was recently profiled on the Institute for the Environment’s “Eye on Earth” blog. The blog post highlights Professor Gulliver’s work studying stormwater runoff.

Professor Gulliver is an expert on a number of issues related to water. He and his research group use MSI resources to study how hydraulic structures, such as dams and reservoirs, affect the concentration of gases in the water that flows around and over them. The turbulent flow from the spillways in these structures results in a higher percentage of dissolved gases in the water, which affects the fish population. The Gulliver group uses HPC resources to model the turbulent flow. 

posted on November 1, 2013

The 2013 Nobel Prize for Chemistry, awarded in October 2013, recognized accomplishments in computational chemistry by Martin Karplus, Michel Levitt, and Arieh Warshel. These three chemists are credited with the development of multiscale models to complex chemical systems.

Professor Jiali Gao, who is an MSI Fellow, is mentioned in the Nobel Committee’s background materials in the award documentation. The scientific background document states that “the work behind this year’s Nobel Prize has been the starting point for both further theoretical developments of more accurate models and applied studies. Important contributions have been given not only by this year’s laureates, but also by many others” including Professor Gao. The documentation cites an article by Professor Gao that appeared in the book Reviews in Computational Chemistry (“Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials,” J Gao, in Reviews in Computational Chemistry, Eds KB Lipkowitz and DB Boyd, VCH Publishers, New York, 1995, 7:119-185).

Professor Gao has been an MSI Principal Investigator and Fellow since 1999. He uses MSI for several projects related to the computer simulation of chemical and biochemical interactions. During 2013, these projects have included:

  • Molecular dynamics simulations of enzymatic reactions
  • Development of the explicit polarization (X-Pol) potential as a next-generation and quantal force field for biomolecular and materials simulations
  • Developing a simulation system to understand protein diffusion processes in a cellular environment
  • Developing novel computational techniques including mixed molecular orbital and valence bond (MOVB) and block-localized density functional theory (BLDFT) and applications to modeling solvent effects on SN2 reactions and the choice of geometrical and energy-gap solvent reaction coordinates in potential of mean force calculations


The Department of Chemistry has posted an article about Professor Gao on their website. The article also links to the Nobel Commitee’s background document.


posted on November 1, 2013

On Wednesday, November 6, from 04:00 - 15:00, MSI Staff will perform scheduled maintenance and upgrades to the network and various systems.

During this maintenance period, we will be performing the following updates:

  • Network firmware updates and modifications will be performed affecting external connectivity for up to 1 hour.
  • Infrastructure services (LDAP, MSI website, email, license servers, etc) will be restarted.
  • Servers hosting websites and databases will be restarted.
  • Galaxy, NX servers, GPUT, SAS, Timelogic decypher servers will be restarted.
  • Torque/moab server for the lab queue will be replaced.
  • Lab scratch space (/scratch1, /scratch2, etc) moved to a new fileserver.
  • Koronis system will be unavailable for a PBSpro upgrade


Systems status is always available on our Status page

If you have any questions, please email



posted on October 29, 2013

Professor Chris Macosko (Chemical Engineering and Materials Science) is a co-leader of a multidisciplinary team researching how to create strong, durable composite materials that are cost-efficient to manufacture. Professor Macosko, an expert in polymers, has been working with Professor Andreas Stein (Chemistry) on a project funded by Artiman Ventures, a Palo Alto venture-capital company that is interested in new techniques for making these materials. The group has developed a technology that involves graphene nanoparticles; this technology has a patent pending through the University of Minnesota and was recently licensed by Adama Materials through the U’s Office for Technology Commercialization. This is the first research sponsored by Minnesota Innovation Partnerships (MN-IP) to have a license deal finalized. An article about this research and how MN-IP helps support the development of new technologies can be found on the OVPR’s Business blog.

Professor Macosko uses MSI resources to process and analyze three-dimensional images of multiphase polymer microstructures.