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Structure-Based Drug Design

Abstract: 
<p>&nbsp;</p> <p><strong>Structure-Based Drug Design</strong></p> <p>This project&rsquo;s goal is to develop and apply new computational methods for structure-based drug design. Previous studies led to the development of the cationic dummy atom approach for molecular dynamics simulations of metalloproteins such as the zinc endopeptidase of botulinum neurotoxin serotype A and the multiple molecular dynamics simulation method for prediction of protein structures as drug targets from genetic sequences and for prediction of synthetically-accessible drug candidates. The researchers are currently testing the practicality of their new methods in identification and optimization of small-molecule reactivators of human acetylcholinesterase and small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, insect acetylcholinesterases, and ribosome inactivating proteins. Successful completion of these projects will lead to new methods for just-in-time drug discovery and ultimately result in therapeutics for treating cancers, infectious diseases, and other medical problems.</p>
Group name: 
pangyp

Modeling Landscape-Scale Meteoric Beryllium-10 Distributions

Abstract: 
<p><strong>Modeling Landscape-Scale Meteoric Beryllium-10 Distributions</strong></p> <p>Meteoric beryllium-10 is a cosmogenically-derived radioisotope with a half-life of 1.5 million years, enabling it to be used as a tracer of long-term geomorphic and landscape change. It therefore offers tremendous power in understanding the cumulative effects of agricultural land-use since the time of European settlement in the Midwestern U.S. However, interpreting measured beryllium-10 concentration in soil profiles and converting them into predictions of erosion rates and soil truncation requires the use of landscape evolution and digital elevation models that require programming expertise and may be computationally intensive. This group is using MSI&#39;s technical expertise to modify existing codes in C++ to run the models as appropriate.</p> <body id="cke_pastebin" style="position: absolute; top: 38px; width: 1px; height: 1px; overflow-x: hidden; overflow-y: hidden; left: -1000px; "> </body>
Group name: 
yook0

Selectivity in Ring-Opening Metathesis Polymerization

Abstract: 
<h4>Selectivity in Ring-Opening Metathesis Polymerization of 3-Substituted Z-Cyclooctenes by Monoaryloxide Pyrrolide Imido Alkylidene (MAP) Catalysts of Molybdenum and Tungsten</h4><p>The synthesis of regio- and stereo- selective polymers by Ring Opening Metathesis Polymerization (ROMP) of 3-substituted cyclooctene has been demonstrated by monoaryloxide ryrrolide imido alkylidene (MAP) catalysts of molybdenum and tungsten. The experimentally found propagating species of such polymerization was found to be opposite to that of what this group previously reported (Martinez, H. et al. <em>ACS Catal</em>., 2:2547 (2012)). Finding an answer for this regio- and stereo- selectivity could lead to a higher control of the polymerization and the synthesis of polymers with well-defined microstructure. The researchers plan to study this by computational calculations using Gaussian 09 package software during each step of the polymerization.&nbsp;</p><p>Return to this PI&rsquo;s <a href="https://www.msi.umn.edu/pi/6275e328e289e4d2e97e5e436507c2f2/7012">main page</a>.</p><p>A bibliography of this group&rsquo;s published research is attached.</p><p>&nbsp;</p>
Group name: 
hillmyer
Attachment: 

Generation of Anatomical Models for Bio-Fluid Mechanics Studies

Abstract: 
<h4>Generation of Anatomical Models for Bio-Fluid Mechanics Studies</h4><p><span style="color: rgb(51, 51, 51); font-size: 14px; background-color: rgb(255, 255, 255); line-height: 1.5;">The purpose of this study is to investigate how the structural properties of lung airways are related to the airway function. The structure refers to the geometry and material properties of the airway walls. The function of the airways include air flow and particle transport. Physical models of human airways will be generated by reconstructing the bronchial tree of real patients imaged by X-ray CT (Computed Tomography), then 3D printing them at life size. In order to obtain the geometry of the anatomy, the software Mimics (Materialize) will be used to segment the CT scans and to generate the constructive details needed for manufacturing and assembling. Successively, flow studies will be conducting on the physical models by magnetic resonance imaging.</span></p><p><font color="#333333">Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/6e528379b0a19bd50d38402c05ee3bd7/10774">main page</a>.</font></p>
Group name: 
colettif

Accessibility Observatory

Abstract: 
<h4>Accessibility Observatory</h4><p><span style="color: rgb(51, 51, 51); font-size: 14px; background-color: rgb(255, 255, 255);">The Accessibility Observatory at the University of Minnesota is focused on the research and application of accessibility-based transportation system evaluation. The Observatory is guided by a threefold mission: to advance the field of transportation system evaluation through research of new data sources and methods for accessibility evaluation; to develop standards and tools to facilitate the use and communication of accessibility-based metrics in transportation planning, engineering, and evaluation; and to apply their tools and expertise in support of continual improvements in the planning, design, engineering, and analysis of transportation systems. Researchers plan to test using MSI to speed computation times on some of their graph building processes.</span></p><p><span style="color: rgb(51, 51, 51); font-size: 14px; background-color: rgb(255, 255, 255);">Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/a189fba615ce0aa1bf26a242aec0be42/10733">main page</a>.</span></p><p>&nbsp;</p>
Group name: 
levinson

Equine Genetics and Genomics

Abstract: 
<h3 class="red">Equine Genetics and Genomics</h3><p>These researchers are using MSI for several projects. The first set of projects involves genome-wide association studies (GWAS) on datasets generated from the SNP genotyping arrays. They are using variants discovered from whole genome sequence (WGS) to impute from low density (54,000) to higher density ~500,000 variants for GWAS. This work is being done on MSI computers.</p><p>The researchers are also using whole-genome sequence data to discover novel variants for follow-up after GWAS for four different phenotypes. They are also developing new SNP genotyping arrays for the horse (both a 2 million and 670 thousand arrays). MSI resources are used for the analysis of genotyping data from test populations.</p><p>The researchers also have three different projects where they are using RNA-seq for transcriptome and gene expression analysis.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/fab8df6dd316e36d11660cda03bfe64d/10141">main page</a>.</p>
Group name: 
mccuem

Plant Speciation and Evolution

Abstract: 
<h3 class="red">Plant Speciation and Evolution</h3><p>This group studies plant evolution and genomics. Current research focuses on two groups - sunflowers (<em>Helianthus</em> spp), and rosinweed (<em>Silphium</em> spp). The researchers are developing a draft genome for the woodland sunflower (<em>Helianthus divaricatus</em>) in the next few months. This is a large genome (3 GB) and its sequencing and assembly will require large computational resources. The group will follow up on this reference genome development with whole-genome resequencing of many individuals, as well as extensive genotyping by sequencing experiments to help map genes involved in speciation, adaptation, and pereniality. The researchers are also moving forward with the development of a reference transcriptome for <em>Silphium</em>, which they will follow up with GBS experiments and transcriptome resequencing of many individuals.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/8dcd6203bcc3577e0e0a72be271a7e6f/10680">main page</a>.</p>
Group name: 
brandvai

Genomics, Metagenomics, and Transcriptomics of Fungal Pathogens of Invertebrates

Abstract: 
<h3 class="red">Genomics, Metagenomics, and Transcriptomics of Fungal Pathogens of Invertebrates</h3><p>Using a combination of next generation sequencing, phylogenomics, genetics, and natural products chemistry, the Bushley lab examines the evolution, diversity, and functions of fungal secondary metabolites. Current research projects utilizing MSI resources include:&nbsp;</p><ul><li>A comparative population genomic study of the evolution of NRPS secondary metabolites among strains of the beetle pathogen and cyclosporin producing fungus <em>Tolypocladium inflatum</em> using PacBio sequencing</li><li>A comparative genomic and transcriptomic analysis of interactions of insect pathogenic and endophytic fungi with both plant and insect hosts</li><li>A metagenomics study of fungal pathogens of the &nbsp;soybean cyst nematodes to elucidate patterns of distribution in natural and agricultural ecosystems and potential roles in mediating resistance to nematodes</li><li>Metagenomics analyses of tropical endophytic fungi of Papua New Guinea and potential anti-herbivore and anti-cancer activity.</li></ul><p>These research projects utilize HPC computing for de-novo genome sequencing and assembly, RNA-Seq, network analysis, large-scale phylogenomic analyses, and population genotyping.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/db501caadd84bb7ee4c9a6bebfa9ebed/10689">main page</a>.</p>
Group name: 
bushleyk

Discover Evidence of Personalized Health Management to Improve Healthcare Outcomes

Abstract: 
<h3 class="red">Discover Evidence of Personalized Health Management to Improve Healthcare Outcomes</h3><p>For most medical problems, clinical (patient) heterogeneity influences treatment efficacy and results in variations in outcome in one-treatment-fits-all settings. However, an opportunity exists to improve outcomes while reducing costs using currently existing treatments when we understand how clinical heterogeneity influences treatment efficacy and how much of a difference exists among treatment options. Knowledge of how to personalize treatment to account for this clinical heterogeneity is the key to optimizing outcome and improving treatment efficiency.</p><p>Projects by this research group use this opportunity to improve healthcare outcomes, whose evidence is extracted from electronic health records. These projects are:</p><ul><li>Mining personalized Alzheimer&#39;s Disease treatment from data</li><li>Predicting a cognitive decline curve for Alzheimer disease</li><li>Using a data-mining approach to facilitate efficient use of nursing resources</li></ul><p>In general, each project derives evidence of improved-outcome evidence associated with treatment options, patient characteristics, and interactions. They benefit largely from MSI computing resources.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/fa26d1b51412b7c4149dc8343ea29e55/10599">main page</a>.</p>
Group name: 
chic

Enhancing Scalability and Energy Efficiency in Extreme-Scale Parallel Systems Through Application-Aware Communication Reduction

Abstract: 
<h3 class="red">Enhancing Scalability and Energy Efficiency in Extreme-Scale Parallel Systems&nbsp;Through Application-Aware Communication Reduction</h3><p>Accesses to shared data should be synchronized to guarantee correct execution of parallel programs. Synchronization dictates a total or partial order on parallel tasks of execution. Since each synchronization point represents a point of serialization, synchronization can easily hurt scalability of parallel programs. To improve scalability in the face of inevitable synchronization, these researchers propose to relax synchronization. The idea is to eliminate a subset of the synchronization points, and to exploit the implicit noise tolerance of an important class of the future parallel applications &ndash; (R)ecognition, (M)ining, and (S)ynthesis, in mitigating relaxation-induced atomicity violations or data races. This project explores how relaxation can improve the scalability of parallel programs. Relaxation can enhance scalability as long as the relaxation-induced degradation in the accuracy of computing remains at acceptable levels. Accordingly, the researchers start with exploration of the trade-off space of accuracy degradation vs. speed-up.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/8b18467acd9e41cd1c8fb70ccae13d78/10429">main page</a>.</p>
Group name: 
karpuzcu

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