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Computed Pathways of Biomass Molecules

Abstract: 

Computed Pathways of Biomass Molecules

These researchers are using Gaussian to perform calculations of energetics of reactants, products, and intermediates of reaction pathways of biomass-derived compounds.

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Group name: 
dauenha0

Simulating Complex Chemical Systems and Processes

Abstract: 

Simulating Complex Chemical Systems and Processes

The Siepmann group develops a variety of computational chemistry tools including: Monte Carlo algorithms for efficient sampling of macromolecular conformations and spatial distributions in multi-component multi-phase systems; accurate and transferable force fields with multiple levels of resolution; and first principles simulation approaches. The Siepmann group applies these computational tools to investigate self-aggregation, phase behavior, and partitioning in polar and non-polar bulk fluids and in heterogeneous and interfacial systems. In particular, the group’s efforts are directed to investigating:

  • Chromatographic retention processes including various forms of liquid chromatography and size exclusion chromatography
  • The solvation mechanisms in liquid-liquid and supercritical extraction systems and in surfactant solutions
  • High-throughput screening of nanoporous materials for energy applications
  • The nucleation of atmospheric aerosols
  • Structural characteristics of organic chromophores in heterogeneous media
  • First principles simulations of reactive phase equilibria
  • Prediction of PVT properties of interest for enhanced oil and gas recovery

The Siepmann group develops and mostly utilizes their own software programs. Some applications use a parallelization hierarchy where large-scale distribution (for example, 16 independent trajectories at 4 different state points) of small, but long runs (4 to 8 cores for 24 hours) are employed, whereas first principles simulations can efficiently utilize 256 to 8,000 cores.

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Group name: 
siepmann

Message from the Director

The Minnesota Supercomputing Institute (MSI) provides advanced research computing infrastructure and expertise in scientific computing, informatics, and application development to the University of Minnesota research and scholarly community and to external partners across all areas of human inquiry...

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...

Seventh Graders Introduced to Supercomputing

On July 1, Brian Ropers-Huilman, MSI Director of Systems Administration and Technical Operations, spoke to a group of seventh-grade students about MSI, high-performance computing, and programming for computers. The students are taking a class in Math and Programming as part of the Minnesota...

Blue Waters Call for Proposals

The Great Lakes Consortium for Petascale Computation (GLCPC) has issued a call for proposals for allocations on the Blue Waters High-Performance Computing System. Please see the GLCPC website for details on the call for proposals. Note that only principal investigators affiliated with an...

MSI PI David Blank Receives Taylor Service Award

Professor David Blank , an MSI PI from the Department of Chemistry , has received the College of Science and Engineering (CSE) 2016 George W. Taylor Award for Distinguished Service. This award recognizes outstanding service to the University of Minnesota. An article about the award appears on the...

Computational Studies in Cell Motility

Abstract: 

Computational Studies in Cell Motility

Cell locomotion plays an essential role during embryonic development, angiogenesis, tissue regeneration, the immune response, and wound healing in multicellular organisms. Movement is a very complex process that involves the spatial and temporal control and integration of a number of sub-processes, including the transduction of chemical or mechanical signals from the environment, intracellular biochemical responses, and translation of the intra- and extracellular signals into a mechanical response. While many single-celled organisms use flagella or cilia to swim, there are two basic modes of movement used by eukaryotic cells that lack such structures - mesenchymal and amoeboid. The former, which can be characterized as "crawling" in fibroblasts or "gliding" in keratocytes, involves the extension of finger-like pseudopodia and/or broad flat lamellipodia, whose protrusion is driven by actin polymerization at the leading edge. In the amoeboid mode, which does not rely on strong adhesion, cells are more rounded and employ shape changes to move - in effect "jostling through the crowd" or "swimming." Here force generation relies more heavily on actin bundles and on the control of myosin contractility. Leukocytes use this mode for movement through the extracellular matrix when adhesion molecules have been knocked out. However, recent experiments have shown that numerous cell types display enormous plasticity in locomotion, in that they sense the mechanical properties of their environment and adjust the balance between the modes. Thus pure crawling and pure swimming are the extremes on a continuum of locomotion strategies, but many cells can sense their environment and use the most efficient strategy in a given context.

One objective of this research is to understand how shape changes can propel cells, the forces that drive the shape changes, and what determines the efficiency of a stroke. Another objective is to understand the cytoskeletal changes needed to produce the shape changes, beginning with blebbing. Blebs result from actomyosin contractions of the cortex, which cause either transient detachments or local rupturing of the cortex. While much less studied than actin-driven extensions, blebs are used as an alternate mechanism for movement by many cell types, and also play a role during cytokinesis and apoptosis.

Another major aspect of this research concerns the signaling networks that control the dynamic rearrangements of the actin cytoskeleton. The pathways involve Rho GTPases that act as molecular switches that relay extracellular signals, both receptor-mediated signals and mechanical signals transduced via integrin-mediated adhesion to the extracellular matrix. Recent experimental work has shed light on the networks involved, but a synthesis of these results into an integrated model that can predict how the balances between the pathways determine whether the amoeboid or mesenchymal mode prevails is needed.

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Group name: 
othmerhg

IBM Town Hall Meeting, September 20

posted on September 12, 2013 As part of the ongoing selection process for the next HPC system at MSI, MSI has invited top high performance computing vendors to present their high performance computing portfolios and roadmaps to users in a Town Hall setting. IBM will be on-site Friday, September 20...

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