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SUMMARY:MICDE Seminar: Margaret Cheung\, Department of Physics\, University of Houston
DESCRIPTION:Bio: Margaret Cheung is an Associate Professor of Physics at the University of Houston. She graduated from the National Taiwan University with a bachelor’s degree in chemistry and received her Ph.D. in physics from the University of California\, San Diego. She carried out theoretical biological physics and bioinformatics research as a Sloan Postdoctoral Fellow at the University of Maryland and started her lab at the University of Houston in 2006. Professor Cheung’s research is in the field of protein folding inside a cell\, calmodulin dependent calcium signaling\, and quantum efficiency in artificial photosynthetic materials. She is particularly interested in developing coarse-grained models for protein dynamics in crowded systems\, creating multi-physics models that bridge dynamics across wide temporal and spatial scales\, and designing computational algorithms that effectively integrate novel high-performance resources. These systems can then be applied for understanding of biological function and for developing therapeutic strategies. She is a fellow of the American Physical Society and a Senior Scientist at the Center for Theoretical Biological Physics at Rice University. \nMolecular Underpinning of Postsynaptic Calmodulin-dependent Calcium Signaling\nCalcium (Ca2+) is exquisitely utilized by a cell for transducing external stimuli through its gradient of extracellular (~1000 μM) and intracellular (~0.1 μM) concentration. A broad spectrum of Ca2+ signals are encoded by protein calmodulin (CaM) through specific binding with various targets regulating CaM-dependent Ca2+ signaling pathways in neurons. I will focus on binding between CaM and two specific targets\, Ca2+/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng)\, as they antagonistically regulate CaM-dependent Ca2+ signaling pathways in neurons. I will show the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca2+) by integrating coarse-grained models and all-atomistic simulations with non-equilibrium physics. We discovered the molecular underpinnings of lowered affinity of Ca2+ for CaM in the presence of Ng by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca2+ binding loops particularly at C-domain of CaM\, enabling Ca2+ release. In contrast\, CaMKII peptide increases Ca2+ affinity for the C-domain of CaM by stabilizing the two Ca2+ binding loops. Through distinctive structural differences in the bound complexes of apoCaM-Ng13-49 and holoCaM-CaMKII\, CaM’s affinity for Ca2+ is delineated by its progressive mechanism of target binding. I will discuss them in the context of evolution and in the crowded environment. \nProf. Cheung is being hosted by Prof. Geva (Chemistry)
URL:https://micde.umich.edu/event/micde-seminar-margaret-cheung-department-of-physics-university-of-houston/
LOCATION:CHEM 1640\, 930 N University\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Featured Events,MICDE Seminar Series,Seminar
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DTSTART;TZID=America/Detroit:20171019T153000
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SUMMARY:MICDE Seminar: Panos Papadopoulos\, Department of Mechanical Engineering\, University of California\, Berkeley
DESCRIPTION:Bio: Panos Papadopoulos is a Professor of Mechanical Engineering at the University of California\, Berkeley\, and director of the Computational Solid Mechanics Laboratory. After obtaining his Diploma in Civil Engineering from the Aristotle University\, Greece\, he moved to California to pursue his graduate studies. He obtained his M. Sc. and Ph.D. in Civil Engineering from UC Berkeley. His research involves experimental\, analytical and computational studies of several mechanics systems. Prof. Papadopoulus develops and applied the finite element method to problems in biomechanics\, dynamics of pseudo-rigid bodies\, mechanics of continues media\, plasticity\, materials science and contact mechanics. \nMultiscale Modeling in Continuum Mechanics: A connection to the Irving-Kirkwood procedure\nThis talk describes a method for extending the classical Irving-Kirkwood procedure used in statistical mechanics for extracting local fluxes to the problem of continuum-on-continuum multiscale modeling. Expressions for stress and heat flux derived here are contrasted to those obtained using the standard Hill-Mandel approach. The polar nature of the macroscopic solid and the role of multiscale invariance are also addressed in the context of this method. Applications are explored within the finite element-based homogenization of solids. \nProf. Papadopoulos is being hosted by Prof. Garikipati (Mechanical Engineering). If you would like to meet with him please send an email to mcteja@umich.edu
URL:https://micde.umich.edu/event/micde-seminar-panos-papadopoulos-department-of-mechanical-engineering-university-of-california-berkeley/
LOCATION:Johnson Rooms\, Lurie Engineering Center\, 3rd Floor LEC 3213ABC\, 1221 Beal Ave.\, Ann Arbor\, MI\, United States
CATEGORIES:Featured Events,MICDE Seminar Series,Seminar
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DTSTART;TZID=America/Detroit:20171025T150000
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SUMMARY:MICDE Seminar: Irina Tezaur\, Extreme Scales Data Science and Analytics Department\, Sandia National Laboratories
DESCRIPTION:Bio: Dr. Irina Tezaur (f.k.a. Dr. Irina Kalashnikova) is a Principal Member of Technical Staff (PMTS) in the Extreme Scales Data Science & Analytics Department (Org. 8759) at Sandia National Laboratories in Livermore\, CA. Prior to joining this group\, from October 2011 to September 2014\, she was SMTS in the Computational Mathematics Department (Org. 1442) at Sandia in Albuquerque\, NM. She received her Ph.D. in Computational and Mathematical Engineering (CME) from Stanford University in 2011. Her advisor at Stanford was Professor Charbel Farhat and I was a member of the Farhat Research Group (FRG). Her Bachelors and Masters degrees are in pure mathematics\, awarded by the University of Pennsylvania in 2006. Dr. Tezaur’s research interests are numerical solution to PDEs\, mixed/hybrid finite element methods\, stability and convergence properties of numerical methods\, Reduced Order Modeling (ROM) and simulation-based analysis of fluid-structure interaction that she currently applies to climate modeling. \nNext-generation modeling & simulation of large-scale ice sheets towards probabilistic sea-level change projections\nRecent observations show that both the Greenland and Antarctic ice sheets are losing mass at increasingly rapid rates [1]. In its fourth assessment report (AR4)\, the Intergovernmental Panel on Climate Change (IPCC) declined to include estimates of future sea-level change from dynamics of the polar ice sheets due to the inability of ice sheet models to mimic or explain observed dynamic behaviors\, such as the acceleration and thinning then occurring on several of Greenland’s large outlet glaciers [2]. In recent years\, there has been a push to develop “next generation” land-ice models and codes for integration into global Earth System Models (ESMs). Unlike their predecessors\, these codes: (1) are able to perform realistic\, high-resolution\, continental scale simulations\, (2) are robust\, efficient and scalable on next-generation hybrid systems (multi-core\, many-core\, GPU\, Intel Xeon Phi)\, and (3) possess built-in advanced analysis capabilities (e.g.\, sensitivity analysis\, optimization\, uncertainty quantification). This talk will give an overview of the Albany/FELIX (Finite Elements for Land Ice eXperiments) [3] next-generation land-ice dynamical core (dycore) that is under development at Sandia National Laboratories as a part of a Department of Energy (DOE) SciDAC-funded project aimed at providing probabilistic sea-level projections from extreme-scale ice sheet and earth system models. This dycore is currently being integrated in to the DOE’s Acelerated Climate Model for Energy (ACME)\, which will be used to calculate anticipated 21st sea-level change projections\, including uncertainty bounds. It is widely accepted that land-ice behaves like a very viscous\, shear-thinning\, non-Newtonian fluid\, similar to lava flow. Typically\, ice sheets are modeled using a quasi-static model in which a steady momentum-balance system for the ice velocities is coupled to dynamic equations for the ice thickness and temperature. The Albany/FELIX dycore is based on the so-called “First-Order Stokes” equations for the ice momentum balance [4]\, an attractive alternative to the more expensive “Full Stokes” model because of its reduced computational cost. Following an overview of our land-ice model and project\, I will describe some of the algorithms and software we have developed as a part of this project that have contributed to our dycore’s robustness and scalability. These include: robust automatic-differentiation-based nonlinear solvers\, scalable algebraic-multigrid-based iterative linear solvers [5]\, adaptive mesh refinement capabilities\, and stable semi-implicit First-Order Stokes-thickness coupling methods. I will also discuss some of the advanced analysis capabilities in Albany/FELIX\, namely a large-scale inversion approach we have developed for obtaining optimal ice initial conditions [6]\, our workflow towards quantifying uncertainties in land-ice models\, and performance-portability of the Albany/FELIX code to new and emerging architectures using the Kokkos library [7]. I will show results which demonstrate that the Albany/FELIX dycore is scalable\, fast and robust for production-scale land-ice problems on state-of-the-art HPC machines. I will also discuss results from a recent validation study in which Albany/FELIX was used to simulate the Greenland ice sheet during the period 1991-2013 with realistic climate forcing\, and the simulation data were compared with observational data collected by NASA satellites [8]. \nThis work was done in collaboration with Irina Demeshko\, Mike Eldred\, Matt Hoffman\, John Jakeman\, Mauro Perego\, Steve Price\, Andy Salinger\, Ray Tuminaro and Jerry Watkins. \nDr. Tezaur is being hosted by Prof. Garikipati (Mechanical Engineering). If you would like to meet her please email mcteja@umich.edu \n[1] I. Velicogna. Increasing rates of ice mass loss from the Greenland and Antarctic ice sheets revealed by GRACE. Geophysical Research Letters\, 36 (19) L19503\, 2009.\n[2] S. Solomon\, D. Qin\, M. Manning\, Z. Chen\, M. Marquis\, K. Averyt\, M. Tignor\, H. Miller. Climate change 2007: The physical science basis\, Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change\, Cambridge Univ. Press\, Cambridge\, UK\, 2007.\n[3] I. Tezaur\, M. Perego\, A. Salinger\, R. Tuminaro\, S. Price. Albany/FELIX: A Parallel\, Scalable and Robust Finite Element Higher-Order Stokes Ice Sheet Solver Built for Advanced Analysis\, Geosci. Model Develop. 8 (2015) 1-24.\n[4] J.K. Dukowicz\, S.F. Price\, W. Lipscomb. Consistent approximations and boundary conditions for ice-sheet dynamics from a principle of least action. J. Glaciol.\, 56 (197) (2010) 480-496.\n[5] R. Tuminaro\, M. Perego\, I. Tezaur\, A. Salinger\, S. Price. A matrix dependent/algebraic multigrid approach for extruded meshes with applications to ice sheet modeling\, SIAM J. Sci. Comput. 38 (5) (2016) C504-C532.\n[6] M. Perego\, S. Price\, G. Stadler. Optimal initial conditions for coupling ice sheet models to earth system models\, J. Geophys. Res.\, 119 (2014) 1894-1917.\n[7] H.C. Edwards\, C.R. Trott\, D. Sunderland. Kokkos: Enabling manycore performance portability through polymorphic memory access patterns. J. Par. and Distr. Comput.\, 74 (12) 3202–3216\, 2014.\n[8] S. Price\, M. Hoffman\, J. Bonin\, T. Neumann\, I. Howat\, J. Guerber\, I. Tezaur\, J. Saba\, J. Lanaerts\, D. Chambers\, W. Lipscomb\, M. Perego\, A. Salinger\, R. Tuminaro. An ice sheet model validation framework for the Greenland ice sheet\, Geosci. Model Dev. 10 (2017) 255-270
URL:https://micde.umich.edu/event/micde-seminar-irina-tezaur-extreme-scales-data-science-analytics-department-sandia-national-laboratories/
LOCATION:1006 H.H. Dow\, 2300 Hayward St\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Featured Events,MICDE Seminar Series
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