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In this tutorial you will learn about the data storage systems available for academic research at the University of Minnesota.

Computer-Aided Design of VLSI Circuits

Abstract: 

Computer-Aided Design of VLSI Circuits

These researchers use MSI supercomputing resources to solve problems in the domain of computer-aided analysis and optimization of VLSI designs. Specifically, the projects will address two problems described below.

  • Impact of thermal-mechanical effects on circuit performance in sub-micron planar and 3D-IC technologies: In 3D-IC technology, dies are stacked vertically and thick cylindrical shaped copper pillars (through silicon vias, TSVs) are used to connect the circuits on different layers. During manufacturing, both silicon and copper TSVs undergo annealing process with a temperature ramp from 250 degrees down to room temperature. However, due to the coefficient of thermal expansion (CTE) mismatch between copper and silicon, thermal residual stress develops inside silicon that impacts the transistor electrical properties and thereby system timing performance. This project is looking into methods for modeling these effects and capturing their impact on circuit performance. In addition, the researchers are also developing modeling and optimization methods for new transistor structures called FinFETs that use a fully three-dimensional structure along with intentional stressors inserted to enhance performance.
  • Electromigration-aware power delivery network analysis: Electromigration has become a serious reliability issue while designing VLSI circuits in current technologies. There is a growing need to accurately model the effects of electromigration and then use this model within the design flow of VLSI circuits. Current models for electromigration are simple and inaccurate, and these researchers aim to come up with electromigration model for the interconnects (metal wires) in the power delivery network that is computationally efficient while physically accurate, and further apply the model to analyze the power delivery network, which typically has hundreds of thousands of metal wires for a single chip. Electromigration is also intimately linked with on-chip residual stress due to CTE mismatches between various constituents of the chip, as well as the stress build-up due to the gradient of atomic concentration. The goal of this project is to analyze the impact of these effects.

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Group name: 
sapatnek

LCSE-MSI Visualization Laboratory (LMVL)

About the LMVL The LMVL is located in room 125 in Walter Library. It is set up for high definition presentations and interactive graphical analyses of very large or complex systems and data through the use of high performance networking, storage, and computational resources. The LMVL systems are...

Genomic Analysis of Inheritance in Maize

Abstract: 

Genomic Analysis of Inheritance in Maize

The Springer lab uses genomic technologies such as high-throughput sequencing to study the molecular sources of phenotypic variation. Their research aims to understand how variation in gene expression levels or epigenetic modifications contributes to phenotypic differences in maize. The current focus of their research is performing DNA methylation profiling and expression profiling for a set of over 100 diverse maize lines in order to associate epigenetic changes with altered gene expression levels or phenotypes. MSI software and computer labs have been used to perform data analyses and visualization of complex datasets.

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Group name: 
springer

LAPACK

Software Support Level: 
Secondary Support
Software Description: 

LAPACK provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.  It has been designed to be efficient on a wide range of modern high-performance computers.

On Linux systems, we recommend the use of the Intel Math Kernel Library (MKL) when LAPACK is needed because these libraries have been tuned and yield better performance.  For more information see the instructions for MKL .

 

Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No

International HPC Summer School 2015

The sixth International Summer School on HPC Challenges in Computational Sciences is now accepting applications for this summer’s session, which will be held June 21-26, 2015, in Toronto, Canada. Graduate students and post-docs from Canada, Europe, Japan, and the U.S. are invited to apply. The...

Molecular Computing

Abstract: 

Molecular Computing

Clock distribution networks are a significant source of power consumption and a major design bottleneck for digital circuits, particularly with increasing variability. Completely asynchronous design methodologies have been studied for decades, but these have never gained widespread acceptance. These researchers have proposed an alternative: splitting digital circuitry into small blocks and synchronizing these locally with independent, cheap clocks (generated with simple inverter rings). This is feasible if one adopts a stochastic representation for signal values. Logical computation is performed on randomized bit streams, with signal values encoded in the statistics of the streams. This project is exploring extensions and applications of these ideas to molecular computing. DNA-based computation via strand displacement is the target experimental chassis.

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Group name: 
riedelm

Computational Magnetics

Abstract: 

Computational Magnetics

This group performs calculations of magnetic properties useful for applications, particularly Spin-Torque RAM (ST-RAM) and magnetic recording. They are using MSI resources for two purposes: Finite difference time domain (FDTD) simulations of light propagation from a near field transducer, as used for heat-assisted magnetic recording (HAMR), and electronic structure calculations of magnetic damping, which is important for ST-RAM. In both cases, the researchers calculate the simple (or lower resolution cases) on their workstations, but need the resources of MSI for calculations requiring more memory. If successful, the impact of the work will be better optical designs for near field transducers and media, and lower energy ST-RAM. Both yield higher density storage/memory.

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Group name: 
victorar

Computational Surface Chemistry

Abstract: 

Computational Surface Chemistry

The structure and dynamics of interfaces control many processes in chemistry and chemical engineering. These researchers use classical molecular dynamics and quantum mechanical/molecular mechanics (QM/MM) methods to investigate the atomic nature of chemical interfaces in multiple contexts. Self-assembled monolayers provide a controllable semi-crystalline surface that they can tailor to exhibit a variety of functionalities spanning the range from completely hydrophobic to mixed surfaces to protic, hydrophilic surfaces that can hydrogen bond with the solvent. The group will exploit the tunable nature of these molecular surfaces to use them as models for such diverse applications as protein-water interfaces and hydrophobic interfaces used in froth flotation for industrial mining. By incorporating functional groups along the surface that are sensitive to the dynamic environment at the interface, they will monitor conditions such as surface field effects and alignment, solvent accessibility in rough molecular surfaces, and surface motion and clustering. This work is performed in close collaboration with experimental researchers to validate the calculations and guide future investigations.

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Group name: 
layfield

Computational Biochemistry and Proteomics

Abstract: 

Computational Biochemistry and Proteomics

This research group is involved in two major projects and uses MSI software resources for routine applications.

  • One project focuses on anti-cancer and antimicrobial drug design that target enzymes like the proteasome or integral membrane proteins like cell surface growth receptors and transporters. For example, inhibition of the proteasome leads to cancer cell apoptosis or programmed cell death. This project requires access to the molecular modeling and simulation resources to perform molecular docking (e.g., with AUTODOCK and DOCK) and QSAR studies (e.g., with Tripos Sybyl , GAUSSIAN, and the Cambridge Structural Database) to guide the synthesis of novel hybrid inhibitors with some similarity to known scaffolds. Similar methods will be applied to other anti-microbial compounds.
  • The second project is to identify the structure and function of a novel family of membrane-bound aspartyl proteases. This uses molecular modeling and simulation resources (e.g., Discovery Studio (Accelrys, Inc.) and PyMOL software packages) and will use structural biology resources (e.g., molecular dynamics software (Gromacs and NAMD) designed for biomolecular systems, biological force fields (CHARMm and AMBER), and docking software (AUTODOCK and DOCK)) in the future to perform docking studies in order to elucidate the preferred protein substrates for these proteases. In addition, this lab collaborates with the Center for Mass Spectrometry and their data are being stored on shared MSI/Mass Spec resources. They use a variety of the proteomics software packages (e.g., MAXQUANT, TINT, X! TANDEM, MASCOT, Scaffold Q+,and ProteinPilot ) for analyzing mass spectrometry data to identify proteins cleaved by their proteases.

In routine applications, the lab uses the Vector NTI software package for molecular biology and genetic engineering applications, the software for data analysis, curve fitting, and graphing (e.g., Origin Lab software and GraphPad Prism), and MATLAB and Mathematica for numerical computation.

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Group name: 
johnsonj

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