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Computational Studies of Proteins of Biomedical Significance

Abstract: 

Computational Studies of Proteins of Biomedical Significance

The overall goal of this research is to understand how the function of proteins of biomedical significance is affected by perturbations either deriving from the environment (such as solvent effects and binding of small molecules) or internal to the protein (such as residue mutation and oxidation). To achieve this goal, these researchers employ a combination of molecular dynamics computer simulations and quantum mechanical calculations to study how the perturbations affect the protein’s structure and dynamics. They are currently working on four projects using MSI.

  • Understand how the allosteric coupling between dystrophin domains is affected by the local solvent environment and by mutations.
  • Identify the mechanism by which allosteric effectors inhibit HIV-1 protease, and test whether the inhibition is additive to the one deriving from orthosteric drug binding.
  • Determine the possible mechanisms by which amino acid oxidation affects protein function by studying the effects of methionine oxidation on the structural dynamics of small peptides and calmodulin.
  • Quantify the effect and identify the mechanism by which amino acid mutations shift the redox potential of azurin

Addressing these problems will help in the development of new targeted therapeutic solutions for the associated health conditions.

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Group name: 
cembran3

High-Resolution Climate Projections to Aid Planning Efforts

Abstract: 

High-Resolution Climate Projections to Aid Planning Efforts

Minnesota’s climate is changing, as indicated by observed temperature increases and extremes in precipitation. These changes are impacting valuable resources, such as swimmable, fishable lakes and rivers; productive forests that sustain iconic species, like moose and birch; fertile farmland cultivated for local food systems and commodity export; and many aspects of the built environment that support our daily lives, such as roads and bridges, stormwater/sewer infrastructure, potable water supply, and power utilities. Projections at the local level of further change in temperature, precipitation, and other weather-related variables are urgently needed by researchers, planners, engineers, farmers and businesses to ensure sound planning and implementation of appropriate adaptation strategies for maintaining and protecting our natural environment, built infrastructure, economy and health. The goals of this project are: to produce high-resolution (areas equivalent to a quarter size of a township) climate model projections for the entire state of Minnesota; to develop a publicly-accessible web-based portal for obtaining the data; and to develop educational resources and train professionals on using and interpreting the data for planning and adaptation purposes.

The focus of the work using MSI resources involves examination of how climate change will affect the climate of Minnesota using high-resolution downscaled climate model projections. The researchers use a computational technique called dynamical downscaling with the Weather Research and Forecasting Model (WRF) to take global climate models projections used by the Intergovernmental Panel on Climate Change to produce new high-resolution climate model projections for the entire state of Minnesota from 1970 to 2099. Over a three year period, ten high-resolution climate projections will be produced for Minnesota that represent moderate and high emission scenarios of projected climate change. This approach will provide a lower and upper bound of plausible outcomes for planning purposes. Model results will be produced statewide at 5 km x 5 km resolution with data available for different time frames.

The group also plans to use the CESM1-CAM5 model, a state-of-the-art climate model produced by the National Center for Atmospheric Research in Boulder, C. This model is being used to investigate the larger-scale role that global forcings have on producing atmospheric conditions leading to droughts in Minnesota. For example, it is recognized that tropical Pacific sea surface temperature anomalies are known to produce persistent blocking highs over the western two-thirds of the U.S. in summertime. The climate model will be used to explore these drivers of drought and to then use the results of the model to drive the regional scale model (WRF).

A Research Spotlight about this group's work appeared on the MSI website in June 2014.

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Group name: 
snyderpk

Harnessing River Power

posted September 19, 2013 St. Anthony Falls Laboratory announced recently that they are collaborating with industry on a project to harness the power of the East River in New York City. This effort, which is being funded by a two-year grant from the National Science Foundation , will involve high-...

Investigating Highly Frustrated Quantum Magnets

In the past few decades, researchers specializing in condensed matter physics have been intensely interested in studying the properties of strongly correlated quantum many-body systems, which are systems on the microscopic scale that include more than two particles that interact with each other...

MSI PIs Honored for Groundbreaking Research

Two MSI PIs from the Department of Computer Science and Engineering , Professor George Karypis and the late Professor John Riedl, will receive the 2016 Seoul Test of Time Award at the World Wide Web Conference in Montreal, Canada later this month. Professors Karypis and Riedl, along with Professor...

Open Science Grid User School 2016

The Open Science Grid (OSG) User School is soliciting applications for students to attend the 2016 session, July 25-29, 2016. This school is intended for researchers who want to learn how they could use high-performance computing in their work. The school takes place on the campus of the University...

Anaconda

Python is a high level programming language that aims to combine remarkable power with very clear syntax. Anaconda is a free cross-platform Python distribution from Continuum Analytics . It comes built in with various scientific Python packages such as NumPy, SciPy, Pandas, Matplotlib, Numba, etc.

Debt Constraints and Employment

Abstract: 

Debt Constraints and Employment

During the past recession, regions of the United States that experienced the largest declines in household debt to income also experienced the largest drops in consumption and employment. These researchers are developing a search and matching model that reproduces such patterns. Tighter debt constraints raise workers' and firms' discount rates, thus reducing match surplus, vacancy creation, and employment. Two ingredients of this model, on-the-job human capital accumulation and worker debt constraints, greatly amplify the drop in employment. On-the-job human capital accumulation implies that the returns to posting a vacancy are backloaded so the surplus from a match is more sensitive to changes in firm discount rates. Worker debt constraints amplify these effects further by preventing wages from falling too much. These researchers show that the model reproduces salient cross-sectional features of the U.S. data, including the comovement between consumption, house prices, and debt-to-income, as well as tradable and non-tradable employment.

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Group name: 
pastorin

How do I get help using MSI's software? What tutorials are available?

Consultants and analysts at MSI provide assistance with software questions depending on the service level of software . Please contact MSI by email help@msi.umn.edu to inquire about getting one-on-one time with an MSI consultant. MSI hosts tutorials on various topics, including computational...

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