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High-Throughput Microscale Assays for Vascular Contractility and Remodeling

Abstract: 

High-Throughput Microscale Assays for Vascular Contractility and Remodeling

Tissue engineered models of muscular contraction and remodeling are necessary to relate in vivo function to in vitro experimental platforms. These researchers are developing an assay that will improve upon previous muscular thin film (MTF) methods developed to measure contractility of cardiovascular smooth and striated muscle in vitro. This assay will be employed to determine the effects of growth factor stimulation on remodeling of tissues subjected to pressure pulses simulating blast traumatic brain injuries. The researchers employ soft lithography techniques, such as microcontact printing, to provide guidance cues for tissue organization in order to engineer realistic in vitro tissue mimics. Previously, MTFs have been used to characterize the effect of blast-like vascular injury in the initiation of cerebral vasospasm. The researchers are combining the current MTF assay with a traction force microscopy approach that will allow significant increases in experimental efficiency. New methods for microcontact printing will be developed and employed to construct arrays with multiple MTF-like tissue constructs whose mechanical function can be tested simultaneously using fluorescent beads and confocal microscopy. Imaris or a memory-intensive MATLAB digital image correlation code will be used to track bead positions, yielding datasets that can be used to determine the mechanical properties of the tissues. The researchers will create arrays of structurally identical tissues for high-throughput screening of growth factor-stimulated perturbation of vascular function. They expect to find a link between platelet-released growth factors and the progression from hypercontractility to large-scale remodeling typical of cerebral vasospasm onset. This assay will provide a platform for development of therapeutics for cerebral vasospasms caused by blast traumatic brain injury.

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Group name: 
alfordpw

Computer & Visualization Labs

Laboratories In addition to providing supercomputing facilities, MSI also has five computational laboratories: All MSI labs have 24 hour continuous access via UCard reader. Lab workstations have access to MSI software, and shared global filesystems. Scientific Development and Visualization...

Ceph in HPC Environments at SC16

Overview Individuals from MSI , RedHat Inc. , Intel Corp ., Indiana University (Jetstream), Laureate Institute for Brain Research , University of Michigan Advanced Research Computing Technology Services came together at SC16: The International Conference for High Performance Computing, Networking,...

Transforming Semiautomatic Patient-Specific Model Building Workflows Into Autonomous Imaging-Through-Analysis Tools

Abstract: 

Transforming Semiautomatic Patient-Specific Model Building Workflows Into Autonomous Imaging-Through-Analysis Tools

While finite element simulations are well established in medical research, their potential for everyday use in clinical practice still lies largely idle. One of the major reasons is the process of building patient-specific computational models, including transfer of diagnostic imaging data to explicit surfaces, geometry cleanup, and boundary-fitted mesh generation. Although powerful software solutions to streamline this process are available today, many simulation workflows involving complex physiological geometries still require the intervention of specially trained analysts. The associated cost and time implications do not fit into many clinical processes characterized by tight budgets and urgent decision-making.

This research program envisions seamless imaging-through-analysis procedures that enable the full automation of predictive biomedical simulations from reading in diagnostic imaging data to the output of clinically relevant simulation results. The goal of the project is to initiate research activities that provide a pathway to a closer integration of predictive simulation in clinical decision-making and help unlock its potential in clinical routines, with transformative impact on improving public healthcare. Clinical applications the group is currently working on include liver perfusion, heart valve hemodynamics, and multiscale bone fracture and osteoporosis diagnosis. They have also successfully started to translate some imaging-through-analysis procedures to applications in materials science, where imaging technologies play a significant role, e.g., to characterize complex microstructure in the degradation analysis of lithium-ion batteries during cyclic charging/discharging.

The group implements practicable cyberinfrastructure frameworks for fully automated simulation workflows. They strive to minimize the implementation effort by consistently leveraging and integrating existing software, in particular open-source tools for image processing (e.g., ITK), adaptive mesh generation (e.g., Netgen), parallelization (Trilinos, PetSc), and visualization (ParaView). The basic entity of their pipeline from geometric parameterization to multiphysics simulation to visualization is an adaptive finite element mesh, which facilitates interoperability between single components. They target both medium-scale computing clusters affordable to hospitals and clinics for simulations in clinical practice, as well as high performance computing environments for extreme-scale research simulations. The heterogeneous features of Mesabi make it the ideal environment to test the potential of the group's software frameworks at different scales (from medium-scale computations that could potentially be carried out on site in a hospital to extreme scale computations), exploiting the local availability of GPUs at each processing unit for extremely efficient operations.

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Group name: 
schillin

Utilizing Computer Modeling and Simulation Software for the Design of a Next Generation Vehicle

Abstract: 

Using Computer Aided Design to Improve the Safety, Performance, and Environmental Impact for a Small Combustion Vehicle

This group’s research aim is to develop methods for evaluating next-generation vehicle technology. These are technologies intended to make vehicles more fuel efficient and safer. The researchers are using a variety of Computer Aided Engineering (CAE) tools on the supercomputers to design specific subsystems.

  • Fluent and CFX by ANSYS are computational fluid dynamics design tools used to simulate airflow around the vehicle. This allows researchers to calculate the lift, drag, and moments on the car and on important aerodynamic components. The group is optimizing these in order to get the most traction and allow the car to be stable and more aerodynamic.
  • Altair Hyperworks is a mechanical finite element analysis tool. It is being used to analyze novel vehicle chassis structures.  The researchers are evaluating concepts that can reduce the weight of future vehicles without sacrificing safety. Other key parameters that researchers are looking at are the stiffness, cost and ease of manufacturing.
  • Ricardo WAVE is a 1D engine simulation program. It is used to analyze the impact of the intake and exhaust geometry on the overall efficiency of the engine.

Every year, the group's models continue to improve through more rigorous simulation and validation of models. This is done by creating physical models and running similar tests to what was simulated and comparing the results. This allows future vehicles to be designed more precisely so that they can be more fuel efficient and safer.

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Group name: 
kittelso

Computational Fluid Dynamics of Wind and Water Waves for Environmental and Energy Applications

Abstract: 

Computational Fluid Dynamics of Wind and Water Waves for Environmental and Energy Applications

These researchers use MSI computing resources to perform high-resolution simulations of wind and water wave flows using high-fidelity computational fluid dynamics. Water waves, wind, and their interactions are important to many applications, including atmosphere-ocean CO2 exchange in the study of global climate change, offshore wind energy and wave energy, and the trajectory and fate of pollutants at water surface.  Recently, the group has also received funding to study oil spills at sea and in the Great Lakes.

This research uses novel simulation methods developed in the group. Their in-house simulation codes include a high-order spectral method for waves and large-eddy simulation of wind turbulence on wave surface-fitted grid. The simulations resolve wave phases, a feature fundamentally distinct from and has a clear advantage over traditional approaches that are spectral and wave-phase-averaged, in which the wave phase information is lost. Because the flow physics are resolved in a more direct way and with much more details than in previous methods, this study will have a better chance to succeed.

The researchers perform simulations of the wind and wave fields, which involve massively parallel computing and datasets with unprecedented volumes and details. They will address the multi-scale wind and wave fluid dynamics through computations of ocean wave field at relatively large scales (100 km domain size, 5 m resolution for waves) and wind field at relatively small scales (2 km domain size, 2 m resolution for turbulence eddies). The big data from the simulations will establish a physical basis for the mechanistic study of the complex dynamic system of the ocean waves and wind.

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Group name: 
shenl

Scratch Storage

MSI provides large capacity and high performance temporary storage to be used while applications are running on the supercomputer. Depending on the system, scratch storage may be a set-aside area of primary storage (global scratch), or may consist of separate storage attached via fast data links...

Computational Fellowships Available

posted on December 4, 2014 Two opportunities in high-performance computing research are now accepting applications for their programs in 2015. The Computational Physics Student Summer Workshop will be hosted by Los Alamos National Laboratory’s Computational Physics Division, June 8 - August 14,...

University of Minnesota Informatics Institute

Abstract: 

University of Minnesota Informatics Institute

The UMII provides bioinformatics services for the genomics, proteomics, and imaging research community. Five analysts run workflows for high-throughput data and participate in research that involves this type of data.

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Group name: 
neuhause

Three-dimensional computer reconstructions of histological brain preparations and neural network analysis

Abstract: 

Three-Dimensional Computer Reconstructions of Histological Brain Preparations and Neural Network Analysis

The growing success and widespread acceptance of deep brain stimulation (DBS) for Parkinson’s and essential tremor has opened up the possibilities for applying brain stimulation for other neurological disorders and conditions. The Lim lab pushes to develop new neural prostheses for hearing restoration and tinnitus suppression. This research requires parallel experiments in animals and in humans to understand the various ways in which we can electrically stimulate different brain regions to restore normal auditory function in patients suffering from hearing loss and debilitating tinnitus. For the animal experiments, special electrode arrays are implanted into different brain regions and stimulated with various parameters to characterize the corresponding activation effects on neural coding and perception. After each experiment, histological slices are used to reconstruct three-dimensional computational brain models using Rhinoceros software to identify the locations of our electrode arrays. The researchers also perform extensive spiking pattern analysis and correlations across locations to identify how specific brain regions are related to different electrical stimulation brain activation patterns. These results not only help characterize different brain regions but will also help to identify optimal locations for implanting neural implants in future patients. The large data files used to create these brain reconstructions and neural analyses require the high-performance computers available at MSI to ensure effective and efficient creation and manipulations of the various brain and network models. 

Group name: 
limhh

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