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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

Electronic Structure Calculations of Organic Reaction Mechanisms

Abstract: 
<h3 class="red">Electronic Structure Calculations of Organic Reaction Mechanisms</h3><p>The hydroxyl radical (OH) is the most important oxidant in the lower atmosphere, or troposphere. Computational research in the past decade, conducted in part by this lab, has begun to elucidate pathways for OH formation that do not require the direct participation of photons. Many of these pathways involve the generation and decomposition of hydroperoxides, and can account for current deficiencies in regional atmospheric chemistry models. In 2015, the Kuwata lab used MSI resources to address the reactivity of an atmospherically relevant hydroperoxide, the vinyl hydroperoxide formed in alkene ozonolysis. In 2016, MSI resources will be used to treat a wider set of possible vinyl hydroperoxide reactions. The researchers are especially interested in the molecules derived from the ozonolysis of isoprene because isoprene is the most abundant unsaturated hydrocarbon in the lower atmosphere. Their predictions for these reactions could therefore have a huge impact on the understanding of atmospheric chemistry. In particular, if researchers predict significant yields of stable alcohols, this would lower the predicted OH yield of isoprene ozonolysis. The resulting deficit in the OH atmospheric &ldquo;budget&rdquo; would drive a search for additional OH sources.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/e7a289f0ae5699c790ca1d9feac6df87/10651">main page</a>.</p>
Group name: 
kuwatak0

Solar Torsional Oscillation in the Presence of Convection

Abstract: 
<h3 class="red">Solar Torsional Oscillation in the Presence of Convection</h3><p>The torsional oscillation is a perturbation to the differential rotation in the convection zone of the sun that is spatially correlated with sunspot activity. Previous work has examined conditions necessary for the torsional oscillation to propagate through the convection zone using mean-field models with parameterized convection. This project examines the propagation behavior using an axisymmetric magnetohydrodynamic model utilizing explicit convection. Specifically, stationary perturbations will be generated at three different latitudes to provide a direct comparison to previous work. Further, perturbations traveling from a latitude of 45&deg; both poleward and equatorward will be used to assess the effect of motion on the propagation. The resources at MSI are necessary because the simulations are very large. The grid contains 1,500 nodes, and three variables must be computed at each node. Each simulation will last for several million time steps. The code requires the use of an Intel Fortran compiler and MPI.</p><p>Return to this PI&#39;s<a href="https://www.msi.umn.edu/pi/a048abb56f1df0ddc1721965c6d00261/10673">main page</a>.</p>
Group name: 
moskowit

For Healthcare: Interactive Simulation and Modeling, and More

Abstract: 
<h3 class="red">For Healthcare: Interactive Simulation and Modeling, and More</h3><p>These research and development efforts are focused on interactive simulation and modeling methods for healthcare interventions. As a unique interdisciplinary team in the UMN Medical School&rsquo;s simulation programs, these researchers have been working with medical device companies and healthcare providers to develop and license out technology innovations as new medical training tools or curricula. Their research outcomes include new virtual reality simulators that make surgical training more efficient, and consequently enhance patient safety through simulation based training. Physicians and medical students worldwide are now using instruments made at the University to exercise and perfect their clinical techniques.</p><p>Ongoing work include studies in new simulation and visualization algorithms, motion tracking, sensor fusion, machine learning and smart tools for medical applications. As virtual reality, augmented reality, or mixed reality are experiencing promising evolutions in aspects of usability and cost-efficiency, these researchers look forward to integrating new research ideas and technology gizmos into useful instruments addressing actual needs in healthcare practices.</p><p>A Research Spotlight about this PI&#39;s work appeared in <a href="https://www.msi.umn.edu/content/computer-simulations-hydraulic-jumps">March 2016</a>.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/53e1978b4960a020da55906974cf56fd/10719">main page</a>.</p>
Group name: 
medicalsim

MEMS Proportional Pneumatic Valve

Abstract: 
<h4>MEMS Proportional Pneumatic Valve</h4><p><span style="color: rgb(51, 51, 51); font-size: 14px; background-color: rgb(255, 255, 255); line-height: 1.5;">This project involves designing a new type of generic pneumatic valve based on micro-electrical-mechanical-systems (MEMS) technology. The valve utilizes an array of micro-actuators positioned over a matching array of micro-orifices. Several benefits are realized by using this scheme instead of a single large actuator acting on a single large orifice. The three most notable are very low actuation power requirements, very fast response and potentially very low cost. The potential cost benefits are realized by exploiting MEMS batch fabrication technologies. MSI resources are utilized to do computational mechanics flow modeling for the valve</span>.</p><p>A bibliography of this group&rsquo;s publications is attached.</p><p><span style="font-size: 14px; line-height: 1.5;">Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/ec4e80ff741b2de9a4cac84a77662606/10208">main page</a>.</span></p><p>&nbsp;</p>
Group name: 
chasetr
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Molecular Gas Dynamic Simulations

Abstract: 
<h3 class="red">Molecular Gas Dynamic Simulations</h3><p>This group focuses on the numerical simulation of complex gas flows for which the molecular nature of the gas must be explicitly accounted for. Such problems include gas-surface interactions and non-equilibrium flows found in both hypersonics and micro-flows. The group specializes in particle simulation methods such as direct simulation Monte Carlo (DSMC), kinetic Monte Carlo (KMC), and molecular dynamics (MD). Research is split between algorithm development and physical model development for these numerical methods. Research is also focused on coupling these methods with each other and with continuum (CFD) methods in order to efficiently simulate practical flows of engineering interest from a molecular perspective. Such particle methods have the potential to incorporate increasingly realistic and accurate physical models but require significant computational resources, necessitating the use of MSI.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/5b3db9b34e2022ad63a39d3df61b86c6/11641">main page</a>.</p>
Group name: 
schwartz

Design of Selective Histone Deacetylase (HDAC) Inhibitors

Abstract: 
<h3 class="red">Design of Selective Histone Deacetylase (HDAC) Inhibitors</h3><p>Applying the principles of fragment- and structure-based drug design, this project investigates novel structural templates for the discovery of selective HDAC inhibitors. The strategy is to design, synthesize, and screen small fragments with limited structural features. Preliminary biological evaluations of these fragments allow for an expeditious exploration of diverse chemical structures, and provide useful information about the protein-ligand interactions. Subsequent chemical modifications, guided by the observed structure-activity relationship (SAR) and computational modeling, are aimed to optimize the potency and potential selectivity among HDAC isoforms.</p><p>This research was featured in an <a href="https://www.msi.umn.edu/content/creating-compounds-treat-disease">MSI Research Spotlight</a> in January 2015.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/265a3ca425f5ade5d8193e08bebf9e66/10177">main page</a>.</p>
Group name: 
chenlq

Enzymology and Biotechnology of Protein Prenylation

Abstract: 
<h3 class="red">Enzymology and Biotechnology of Protein Prenylation</h3><p>Protein prenylation is an irreversible covalent post-translational modification found in all eukaryotic cells, comprising of farnesylation and geranylgeranylation. Three prenyltransferase enzymes catalyze this modification. This three-step process increases protein hydrophobicity, and often leads to plasma membrane association. Prenylation serves as the first critical step for membrane targeting and binding, as well as mediating protein-protein interactions of a large number of Ras proteins; heterotrimeric G-proteins also require prenylation for activity.Significant interest in studying protein prenylation originally stemmed from the finding that this modification was necessary to maintain malignant activity of oncogenic Ras proteins although now it is known that prenylation is important in a wide ranges of diseases. These researchers are using computer-based methods for three subprojects within this area. They include:</p><ul><li>Design of caging groups used to mask the activity of substrates and inhibitors of protein prenylation</li><li>Bioinformatic analysis of proteomic data obtained using probes that allow selective detection of prenylated proteins</li><li>Modeling of prenyltransferase structures to design mutations that alter substrate specificity</li></ul><p>Return to this PI&rsquo;s <a href="https://www.msi.umn.edu/pi/e78509ed895cdd6a24b95c4d624027fd/24200">main page</a>.</p><p>&nbsp;</p>
Group name: 
distefan

Phylogenetic Analysis of Trait Evolution

Abstract: 
<h3 class="red">Phylogenetic Analysis of Trait Evolution</h3><p>These researchers study the evolution of traits that influence chances of speciation and extinction. Plant mating system is one such trait, because it strongly affects population sizes and distributions of genetic diversity. Geographic range is another such trait because geologic, climatic, and biotic conditions all affect population size and subdivision. Other traits are often associated with these, and it can be challenging to identify the particular traits or trait combinations that most directly affect speciation and extinction.</p><p>This work typically involves two phases of analysis, each of which can be computationally intensive for groups of more than, say, a thousand species. First is constructing a phylogeny of living species from DNA sequence data. Second is fitting models of trait evolution, speciation, and extinction to those phylogenies. Such analyses are easily parallelized, especially when conducted in a Bayesian statistical framework, and so the researchers can readily make use of MSI&#39;s cluster resources.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/628a39756aa21530c874df32294e7cd3/10594">main page</a>.</p>
Group name: 
eeg

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