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Structural Correlates of Personality in Healthy Adults

Abstract: 

Neural Mechanisms of Personality and Decision Making

Psychologists are increasingly focused on identifying the biological substrates of personality traits. One promising method for identifying brain systems associated with personality traits is magnetic resonance imaging (MRI). Functional MRI is used to identify personality traits that are associated with brain processes during specific tasks. However, structural MRI can also be used and has the advantage that hypotheses about many personality traits can be examined simultaneously, because associations of traits with brain structure are not dependent on any specific task. In a previous test of the hypothesis that personality traits would be associated with the volume of specific brain structures, these researchers found support for a model specifying brain systems underlying each of the Big Five personality traits (Extraversion, Neuroticism, Agreeableness, Conscientiousness, and Openness/Intellect). However, this study did not differentiate between volume in gray matter versus white matter, an important anatomical distinction in the brain. Nor did it examine more specific personality traits based on subdivisions of the Big Five, which describe personality at a less general level of resolution and would allow testing of more specific biological hypotheses. The current project uses more finely differentiated measurements of personality traits in conjunction with a more sophisticated assessment of brain structure that parcellates gray and white matter and provides an index of gray matter thickness throughout the cortex. Cortical thickness has been shown to have important correlates, from learning of motor tasks to psychopathology. Assessing cortical thickness from MRI data is a computationally intensive process that can be accomplished using the MRI analysis program FreeSurfer. As this program typically takes up to 48 hours to process data for a single subject, and as this project examines associations of cortical thickness with personality in 300 subjects, the resources of MSI are invaluable. The researchers are also doing a more sophisticated DTI analysis for up to 200 individuals.

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Group name: 
deyoungc

Molecular Dynamics Simulation of Chemical and Biochemical Processes

Abstract: 

Molecular Dynamics Simulation of Chemical and Biochemical Processes

The Gao group is continuing their investigations in several areas, including the interplay between protein dynamics and mechanism of enzymatic reactions; the development of novel quantum mechanical methods for studying energy and charge transfer processes in chemical and biological macromolecular systems; the simulation and modeling of vibrational Stoke shifts of probe molecules in proteins; and solvent effects on chemical reactions and interactions in condensed phases.

The group's approach is based on statistical mechanical Monte Carlo and molecular dynamics simulations, making use of combined quantum mechanical and molecular mechanical (QM/MM) potentials. The first project area involves molecular dynamics simulations of enzymatic reactions including the demethylation reactions catalyzed by an FAD-dependent enzyme and metalloenzymes, the final step in nucleotide UMP biosynthesis by OMP decarboxylase, thiamine-dependent enzymes, and proton-coupled electron transfer (PCET) processes in ribonucleotide reductase and in photosystem II. These studies will provide a deeper understanding of the reaction mechanism and the origin of catalysis. In addition, the group has initiated a study of the ultraviolet-8 activated dimer dissociation of UVR8, which triggers cellular response in plants.

The second project aims at the development of multistate density functional theory for charge transfer, and the explicit polarization (X-Pol) potential as a next-generation and quantum force field for biomolecular and materials simulations. These methods represents novel approaches to describe molecular systems and to determine the potential energy surface, and it goes beyond the so-called combined QM/MM approach, which was awarded by the 2013 Nobel Prize in Chemistry.

The third project is aimed at developing a simulation system to understand the electrostatic environment inside of an enzyme's active site.

The final project area focuses on development of novel computational techniques including mixed molecular orbital and valence bond (MOVB) and an X-Pol based reactive force field and applications to modeling solvent effects on a variety of chemical reactions and reaction networks.

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Group name: 
gaoj

Cluster Lensing With Hubble Frontier Fields

Abstract: 

Cluster Lensing With Hubble Frontier Fields

The primary goal of this project is the reconstruction of sky-projected density distribution within clusters of galaxies. Most of the mass is comprised of dark matter whose distribution cannot be seen directly, so has to be inferred. The inference is done using gravitationally lensed background sources. A typical rich cluster has about 10-100 lensed images. Because this number is relatively small compared to the spatial detail needed for adequate mapping of the clusters, the problem of cluster mass reconstruction is very under-constrained. There are several methods in use that do mass reconstruction, each with its own assumptions and priors.

This group's method is based on a genetic algorithm, called GRALE, which is a free-form, adaptive grid method that uses a genetic algorithm to iteratively refine the mass map solution. It efficiently explores the model space, does not get stuck in local minima, and explores the range of mass uncertainties quite differently from other existing methods. The reconstructed maps are very accurate, but the computation time is large, and only possible on supercomputers.

Given maps of reconstructed mass distribution with accompanying uncertainties, they can be used for two main purposes. One is to discover and examine the very first generation of galaxies that formed in the universe. The light travel time to them is nearly the age of the universe, making them faint and difficult to observe. Most of these are so faint that existing and future telescopes are not adequate. To solve the problem astronomers use "nature's telescopes," clusters of galaxies that act as gravitational lenses to amplify distant sources, by typical factors of between 10 and 50. However, these "telescopes" have very uneven "optics," i.e. mass distributions, hence the need for accurate mass reconstruction.

This research was featured in a Research Spotlight on the MSI website in July 2015.

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Group name: 
willia14

Genomics of Host-Microbiome Interactions

Abstract: 

Genomics of Host-Microbiome Interactions

With the advent of next generation sequencing, it has become possible to examine entire genomes and transcriptomes of humans and other animals with relative ease. These data have been used to validate previously discovered biological mechanisms as well as to discover new phenomena that are implicated in diseases, such as cancer. This technological advance has also opened up new research possibilities by allowing scientists to survey and quantify the microbiome, the collection of microorganisms that reside in and on the bodies of humans and other animals. Again, researchers have leveraged this new source of information to make breakthroughs in human disease that are caused by alterations in the microbiome, including diabetes, inflammatory bowel disease, and obesity. Although the human microbiome is influenced by environmental factors, bacteria also interact with human cells through immune system and metabolic pathways. 

This group's research aims to understand and characterize host-microbiome interactions in a variety of conditions. They have several ongoing projects, aiming to answer the following biological questions:

  • What are the molecular mechanisms controlling host-bacteria interactions? Which genes and pathways are involved in both the host and microbiome side?
  • How does host genetic variation control interactions with our microbiome? What are the effects of different environments and genetic backgrounds across human populations?
  • How did the complex symbiosis between us and our microbiome evolve throughout human history? Can we identify signatures of coevolution in human and microbial genomes?
  • How do host-microbiome interactions control susceptibility to complex disease? What are the unique roles of host genetics, bacterial communities, and environmental exposures?

Each of these research projects involves analyses of large genomic and metagenomic datasets using resources from MSI, including installed software, CPU time, storage space, and the parallel computing environment.

This research was featured in a Research Spotlight on the MSI website in October 2015.

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Group name: 
blekhman

4/9/13: MSI PI Cramer Named CSE Associate Dean

Professor Chris Cramer ( Fellow , Chemistry ) has been named the College of Science and Engineering’s new associate dean for academic affairs, the college announced on April 9, 2013. The appointment will become effective on July 1, 2013. You can read the announcement on the chemistry department’s...

Interview: Makenzie Provorse

Makenzie Provorse is a graduate student in Professor Jiali Gao’s ( MSI Fellow ) group in the Department of Chemistry . She entered the University of Minnesota in the fall of 2009 and joined the Gao group in January 2010. She’s been using MSI since then. Ms. Provorse was a finalist at the 2013 MSI...

A Novel Two-Dimensional Copper-Silicon Material

Image description: Left: Top and side views of a section of a two-dimensional Cu 2 Si monolayer. Cu atoms copper colored, Si atoms grey. Right: Bonding structure of the Cu 2 Si monolayer. (a-c) Individual 4c-2e σ bonds. (d) Superimposition of 4c-2e σ bonds. Copper is orange, silicon is blue. LM...

Huygens

The Huygens System is an image processing software package specifically designed to facilitate the restoration of microscopic images. It provides many arithmetic operations on image types ranging from simple 2D images of unsigned bytes to multi-parameter, 3D time series of complex values. This functionality forms the basis for the more advanced features of the Huygens System aimed at image restoration, i.e., the `reconstruction' of the object that gave rise to the actual recorded image.The Huygens System shows these images in a transparent way and allows inspection, processing and restoration...

Interactive queue use with isub

Notes on isub Use The command isub is an MSI-written wrapper to ssh and qsub, designed specifically for interactive use. When isub is run with default options, it will ssh to a compute node in a pool of nodes reserved for interactive use. These nodes are the lab back-end, so when your shell starts...

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