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[Illinois] Cancer Community Symposium 2012: A Sensitivity Scale for Targeting T Cells with Chimeric Antigen Receptors (CAR) and Bispecific T Cell Engagers (BiTE)
09 May 2012 | | Contributor(s):: Jennifer Stone
Using a patients immune system to target cancer and maintain long-term surveillance is an attractive goal. Although T cells can respond potently to tumors, immune tolerance mechanisms often result in deletion or inactivation of those T cells expressing specific T cell receptors (TCRs) against...
[Illinois] Cancer Community Symposium 2012: DriveRank: Discovering Patient-Specific Driver Mutations
09 May 2012 | | Contributor(s):: Jack Pu Hou
One of the pressing challenges in cancer genomics is to distinguish driver mutations (i.e. mutations involved in tumorigenesis) and passenger mutations (i.e. functionally neutral mutations). Current approaches to identifying driver mutations in cancer look for recurrent events in multiple...
[Illinois] Cancer Community Symposium 2012: Elevated Estrogen Signaling Drives Tumorigenesis in a Novel Animal Model for Ovarian Epithelial Cancer
09 May 2012 | | Contributor(s):: Mary Jo Laws
We generated a mouse model where aberrant estrogen receptor alpha (Esr1) signaling in the hypothalamo-pituitary-ovarian axis leads to ovarian tumorigenesis. In this model, termed Esr1d/d, the Esr1 gene is selectively deleted in the anterior pituitary. The Esr1d/d mice form palpable ovarian tumors...
2010 Nano-Biophotonics Summer School at the University of Illinois at Urbana-Champaign
20 Sep 2010 | | Contributor(s):: Gabriel Popescu, Stephen Boppart, Rohit Bhargava, Logan Liu, Nahil Sobh
The 2010 summer school covers: Principles of Nano-Biophotonics Technology and methods of investigation Current research (e.g. biomolecular sensing, nanoprobes, nonlinear microscopy, nanoscopy, nanoplasmonics)
A Fast Multigrid Approach for Solving the Helmholtz Equation with a Point Source
04 Feb 2016 | | Contributor(s):: Eran Treister
Solving the discretized Helmholtz equations with high wave numbers in large dimensions is a challenging task. However, in many scenarios, the solution of these equations is required for a point source. In this case, the problem can be be reformulated and split into two parts: one in a solution of...
A Massively Parallel Semicoarsening Multigrid for 3D Reservoir Simulation on Multi-core and Multi-GPU Architectures
04 Feb 2016 | | Contributor(s):: Abdulrahman Manea
In this work, we have designed and implemented a massively parallel version of the Semicoarsening Black Box Multigrid Solver , which is capable of handling highly heterogeneous and anisotropic 3D reservoirs, on a parallel architecture with multiple GPU’s. For comparison purposes, the...
A Multigrid Method for the Self-Adjoint Angular Flux Form of the Radiation-Transport Equation Based on Cellwise Block Jacobi Iteration
04 Feb 2016 | | Contributor(s):: Jeffrey Densmore
Cellwise block Jacobi iteration is a technique for radiation-transport calculations in which the angular flux for all directions is solved for simultaneously within a spatial cell with the angular flux in neighboring cells held fixed. Each step of the iteration then involves the inversion of a...
A Performance Comparison of Algebraic Multigrid Preconditioners on GPUs and MIC
04 Feb 2016 | | Contributor(s):: Karl Rupp
Algebraic multigrid (AMG) preconditioners for accelerators such as graphics processing units (GPUs) and Intel's many-integrated core (MIC) architecture typically require a careful, problem-dependent trade-off between efficient hardware use, robustness, and convergence rate in order to...
A Scalable Algorithm for Inverse Medium Problems with Multiple Sources
04 Feb 2016 | | Contributor(s):: Keith Kelly
We consider the problem of acoustic scattering as described by the free-space, time-harmonic scalar wave equation given by (0.1) along with radiation boundary conditions. Here, is a point in , is the source term, and is the wavenumber. Our formulation is based on potential theory....
Accurate Chemical Master Equation (ACME)
20 May 2013 | | Contributor(s):: Youfang Cao, Anna Terebus, John Feser, Nahil Sobh, Jie Liang
Direct solution method of discrete Chemical Master Equation (dCME) for the steady state, the time evolution of full probability landscapes, and the first passage time distribution (FPTD) in biological networks.
Application of Multigrid Techniques to Magnetic and Electromagnetic Systems
02 Feb 2016 | | Contributor(s):: Benjamin Cowan
We discuss the use of multigrid techniques for several novel systems related to electromagnetics. One of these is the magnetostatic problem, in which systems can involve highly anisotropic and nonlinear materials. We describe the linear problems arising in several variations of this problem,...
14 Aug 2006 | | Contributor(s):: Pradeep R. Nair, Jonghyun Go, Graeme John Landells, Tejas Rajiv Pandit, Muhammad Alam, Xin Jin, Piyush Dak, Ankit Jain, Mohammad Ryyan Khan, Mohammad Ryyan Khan
BioSensorLab is a tool to evaluate and predict the performance parameters of Biosensors.
cadnano to PDB File Converter
13 Nov 2013 | | Contributor(s):: Jejoong Yoo, AbderRahman N Sobh, Chen-Yu Li, Aleksei Aksimentiev
Accepts CadNano files in the form of *.json and outputs a file in *.pdb which can be read by programs such as VMD.
Compatible Relaxation Based Geometric-Algebraic Multigrid
02 Feb 2016 | | Contributor(s):: Fei Cao
We develop compatible relaxation algorithms for smoothed aggregation-based multigrid coarsening. In the proposed method, we use the geometry of the given discrete problem on the finest level to coarsen the system together with compatible relaxation to from the sparsity structure of the...
Data-Centric Models for Multilevel Algorithms
05 Feb 2016 | | Contributor(s):: Samuel Guiterrez
Today, computational scientists must contend with a diverse set of supercomputer architectures that are capable of exposing unprecedented levels of parallelism and complexity. Effectively placing, moving, and operating on data residing in complex distributed memory hierarchies is quickly becoming...
DBR Laser Simulator
07 Sep 2012 | | Contributor(s):: Nikhil Sancheti, Lynford Goddard, Christopher Adam Edwards
Describes properties of a GaAs/AlGaAs DBR laser
Discretization of Elliptic Differential Equations Using Sparse Grids and Prewavelets
02 Feb 2016 | | Contributor(s):: Christoph Pflaum
Sparse grids can be used to discretize second order elliptic differential equations on a d-dimensional cube. Using Galerkin discretization, we obtain a linear equation system with unknowns. The corresponding discretization error is in the -norm. A major difficulty in...
DIY BIOSENSORS Summer 2014 Workshop
26 Jun 2014 | | Contributor(s):: Kaustubh Bhalerao
Learn how to build a simple, low cost sensor to detect spoiled milk using simple materials that illustrate cool concepts such as microﬂuidics, sample processing and biodetection.In this project you will design microﬂuidic patterns, construct them out of clear plastic ﬁlm, add...
Geometric Multigrid for MHD Simulations with Nedelec Finite Elements on Tetrahedral Grids
02 Feb 2016 | | Contributor(s):: Chris Hansen
The Magneto-HydroDynamic (MHD) model is used extensively to simulate macroscopic plasma dynamics in Magnetic Confinement Fusion (MCF) devices. In these simulations, the span of time scales from fast wave dynamics to the desired evolution of equilibrium due to transport processes is large,...
High Dimensional Uncertainty Quantification via Multilevel Monte Carlo
02 Feb 2016 | | Contributor(s):: Hillary Fairbanks
Multilevel Monte Carlo (MLMC) has been shown to be a cost effective way to compute moments of desired quantities of interest in stochastic partial differential equations when the uncertainty in the data is high-dimensional. In this talk, we investigate the improved performance of MLMC versus...