[Illinois] Reducing Communication Costs for Sparse Matrix Multiplication within Algebraic Multigrid
04 Feb 2016 | Online Presentations | Contributor(s): Grey Ballard
We consider the sequence of sparse matrix-matrix multiplications performed during the setup phase of algebraic multigrid. In particular, we show that the most commonly used parallel algorithm is often not the most communication-efficient one for all of the matrix multiplications involved. By using an alternative algorithm, we show that the communication costs are reduced (in theory and practice), and we demonstrate the performance benefit for both model and real problems on large-scale...
[Illinois] Space-time constrained FOSLS with AMGe upscaling
04 Feb 2016 | Online Presentations | Contributor(s): Panayot Vassilevski
We consider time-dependent PDEs discretized in combined space-time domains. We first reduce the PDE to a first order system. Very often in practice, one of the equations of the reduced system involves the divergence operator (in space-time). The popular FOSLS (first order system least-squares) method is then applied modified by keeping the divergence equation as a constraint which we refer to as CFOSLS (constrained FOSLS). Applying finite elements to discretize the CFOSLS problem leads to a...
[Illinois] Multilevel Markov Chain Monte Carlo for Uncertainty Quantification in Subsurface Flow
04 Feb 2016 | Online Presentations | Contributor(s): Christian Ketelsen
The multilevel Monte Carlo method has been shown to be an effective variance reduction technique for quantifying uncertainty in subsurface flow simulations when the random conductivity field can be represented by a simple prior distribution. In state-of-the-art subsurface simulation the stochastic model of the conductivity field must be conditioned on observe physical data. Sampling from this complicated distribution is carried out by the Markov chain Monte Carlo method. In this talk we...
[Illinois] Discretization of Elliptic Differential Equations Using Sparse Grids and Prewavelets
04 Feb 2016 | Online Presentations | 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 using this sparse grid discretization is complexity of the related stiffness matrix. Consequently, only differential equations with constant coefficients could be efficiently discretized using sparse...
[Illinois] High Dimensional Uncertainty Quantification via Multilevel Monte Carlo
04 Feb 2016 | Online Presentations | 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 standard Monte Carlo. While both methods converge at a rate independent of the dimension of the stochastic input, the use of a series of nested grids in MLMC allows us to improve the convergence by...
[Illinois] Stable Discretizations and Robust Block Preconditioners for Fluid-Structure Interaction Systems
04 Feb 2016 | Online Presentations | Contributor(s): Kai Yang
In our work we develop a family of preconditioners for the linear algebraic systems arising from the arbitrary Lagrangian-Eulerian discretization of some fluid-structure interaction models. After the time discretization, we formulate the fluid-structure interaction equations as saddle point problems and prove the uniform well-posedness of these formulations. Then we discretize the space dimension by finite element methods and prove their uniform well-posedness by two different approaches...
[Illinois] Nanotechnology meets Biology in the Cancer Cell: Applications in Medicine, Drug Delivery, and Determining Drug Efficacy
04 Feb 2016 | Online Presentations | Contributor(s): Mostafa El-Sayed
Dr. Mostafa El-Sayed received his B.Sc. from Ain Shams University in Cairo; and Ph.D. from Florida State University. He was Postdoctoral Fellow at Yale University, Harvard University and the California Institute of Technology. From 1961-94 he served as a faculty member in the Department of Chemistry and Biochemistry at the University of California Los Angeles; and is currently Julius Brown Chair and Regents’ Professor at the Department of Chemistry at the Georgia Institute of Technology. Professor El-Sayed received the 2007 US National Medal of Science in Chemistry from the President of the United States (2008) and the Medal of the Egyptian Republic of the First Class from the President of Egypt (2009). He was nominated to the US National Medal of Science in Chemistry Committee in 2014, and served a two-year term.
Professor El-Sayed is an Elected Member of the US National Academy of Sciences (1980), an Elected Fellow of the American Academy of Arts and Sciences (1986), an JOINTLY WITH NSF IGERT-CMMB AND NIH/NCI M-CNTC SYMPOSIUM 13 Elected Associate Member of the Third World Academy of Sciences (1984); he is an Inaugural Fellow of the American Chemical Society, the American Physical Society and an Elected Fellow of the American Association for the Advancement of Sciences. He is an Honorary Fellow of the Indian Chemical Society and the Chinese Chemical Society. He received the King Faisal International Prize in the Sciences (Chemistry), (1990); Doctor Honoris Causa from the Hebrew University, honorary Doctor Degrees from the Colleges of Medicine of both Mansoura and Alexandria Universities in Egypt. He has received a number of national awards such as the Fresenius, the Tolman, the Richard’s medal, the Lindeman’s medal, the Seaborg’s medal as well as other numerous local ACS section awards. In 2002, he received the ACS-APS Langmuir National Award in Chemical Physics and in 2007 was awarded the Georgia Tech’s highest award, the distinguished Professor of the year.
Professor El-Sayed was an Alexander von Humboldt Senior Fellow, Germany (1982), a Visiting Professor at the University of Paris, an Alfred P. Sloan as well as a Guggenheim Foundation Fellow, a Fairchild Fellow at the California Institute of Technology and a Miller Visiting Professor at University of California at Berkley.
[Illinois] Rare Events with Large-Impact: Bioengineering & Clinical Applications of Circulating Tumor Cells
04 Feb 2016 | Online Presentations | Contributor(s): Mehmet Toner
Dr. Mehmet Toner is the Helen Andrus Benedict Professor of Biomedical Engineering at the Massachusetts General Hospital (MGH), Harvard Medical School (HMS), and is the co-founding director of the NIH BioMicroElectroMechanical Systems (BioMEMS) Resource Center at the MGH. He received his BS degree from Istanbul Technical University and MS degree from the Massachusetts Institute of Technology (MIT), both in Mechanical Engineering. Subsequently he completed his PhD degree in Medical Engineering at Harvard-MIT Division of Health Sciences and Technology in 1989. He joined the faculty at the MGH and HMS as an Assistant Professor of Biomedical Engineering in 1989, and was promoted to Associate Professor in 1996, and to Professor in 2002. Dr. Toner holds a joint appointment as a Professor of Health Sciences and Technology at the Harvard-MIT Division of HST.
Dr. Toner is internationally recognized for his work at the interface of bioengineering and life sciences especially in the detection of rare circulating tumor cells.
Dr. Toner has published over 350 original papers including in Nature, Science, New England Journal of Medicine, Science Translational Medicine, Nature Biotechnology, and PNAS. He has also delivered over 400 invited, keynote and plenary presentations.
In 1998, Dr Toner was selected to become a Fellow of the American Institute of Medical and Biological Engineering. In 2007, he became a Fellow of the American Society of Mechanical Engineers. In 2012, he was selected to become a Fellow of the Society for Cryobiology. In 2013, he received the H.R. Lissner Medal from the American Society of Mechanical Engineering. He served on the Board of Advisors of the National Science Foundation from 2010-2013.
Dr. Toner serves on the Scientific Advisory Board of multiple biotechnology and medical device companies, and has been involved as a scientific founder of multiple startup companies.
[Illinois] CNST Nanotechnology Workshop 2015
04 Feb 2016 | Workshops | Contributor(s): Mustafa El-sayed, Mehmet Toner
The CNST Nanotechnology Workshop highlights University of Illinois research in bionanotechnology and nanomedicine, nanoelectronics and nanophotonics, and nanomaterials and nanomanufacturing, leading to cross-campus and industry collaborations.
[Illinois] Signal Processing at Light Speed: Ultrashort Optical Pulse Generation with Arbitrary Waveforms
29 Jan 2016 | Online Presentations | Contributor(s): Claire Mcghee
We aim to further improve early detection of cancer biomarkers, including metal ion and small molecules, using functional DNA as the selective component for photonic crystal surface enhanced Raman scattering (PC-SERS) based detection. It is known that gold nanoparticles (AuNPs) display SERS properties and that further enhancement of SERS active nanoparticles can occur when AuNP are deposited on a PC. To create this device we have synthesized AuNP of varying sizes and shapes, to adjust the...
[Illinois] Using Photonic Crystals to Enhance SERS Signals for Early Detection of Prostate Cancer
29 Jan 2016 | Online Presentations | Contributor(s): Caitlin Race
Prostate cancer is the second most common cancer for men, and the second leading cause of death due to cancer in men. Currently, the most common screening method aims to detect high levels of prostate-specific antigen (PSA) in blood. Our research has shown the potential for both better prostate cancer biomarkers and more accurate ways of screening them. This talk will focus on the use of photonic crystals for surface-enhanced Raman spectroscopy (PC-SERS) as a new method for using small...
[Illinois] Manipulating Substrate Topography for Enhanced Myogenic Differentiation of Primary Myoblasts and Neuromuscular Junction Formation
29 Jan 2016 | Online Presentations | Contributor(s): Eunkyung Ko
Myogenic commitment of stem cells and primary myoblasts has drawn attention for developing treatments for skeletal muscle diseases. Biophysical cues as well as biochemical cues are known to influence the cellular mechanism of the myogenic differentiation event. Recent studies have revealed that topography can manipulate cellular functions by guiding the focal adhesions of cells. Substrates with nano and micro scale patterns have been shown to cause contact guidance of cells, thereby,...
[Illinois] Cadherin-Modulated Neural Differentiation of Stem Cells for Neuromuscular Junction Engineering
29 Jan 2016 | Online Presentations | Contributor(s): Ellen Qin
Recently, efforts are increasingly made to engineer NMJ in vitro for both fundamental and applied bioscience studies. Certain success was made to modulate neural differentiation of stem cells using soluble factors and cell adhesion matrix properties. However, these studies were often plagued by the dependency of neural differentiation level on the density of cells plated on a substrate, which implicates an important role of cadherin-modulated cell-cell adhesion in regulating neural...
[Illinois] Role for Stiffness in Vascular Fate
29 Jan 2016 | Online Presentations | Contributor(s): Lian Wong
Stem cells, including embryonic stem cells (ESC) and induced pluripotent stem cells, have been explored as tools for studying development, as well as, potential sources for a large number of therapies in regenerative medicine. Traditionally, ESC are cultured on TC-plastic, however; it has been recently shown that the stiffness of the environmental substrate can direct the cells towards various cell lineages. Our laboratory is interested in examining signaling in vascular cell fate under...
[Illinois] Bionanotechnology Seminar Series
29 Jan 2016 | Series
This series is organized by PhD students who are appointed as Trainees in the NIH/NCI Midwest Cancer Nanotechnology Training Center (M-CNTC) and in the NSF IGERT in Cellular and Molecular Mechanics and BioNanotechnology (CMMB IGERT). These traineeships are designed to train the next generation of leaders who will define the new frontiers of nanotechnology in cancer research and in cellular and molecular mechanics and bionanotechnology. The BioNanotechnology Seminar Series is also sponsored...
[Illinois] Synthetic Optical Holography
26 Jan 2016 | Online Presentations | Contributor(s): Brad Deutsch
Bradley earned a Ph.D. in Optics in 2011 at the University of Rochester’s Institute of Optics. His research involved nanoscale optics, with a Ph.D. emphasis on phase-shifting interferometric methods for near-field optical microscopy and nanoparticle detection. At Beckman he will work with Scott Carney and Rohit Bhargava of the Bioimaging Science and Technology group. Bradley’s project as a Beckman Fellow will focus on developing an ultramicroscopy technique that encodes spatial information in the spectral domain for improved temporal resolution without a loss of spatial resolution, for use in biology, medicine, and imaging applications.
[Illinois] Dimeric Trigger Responsive Drug Conjugate for High Loading Nanoencapsulates
26 Jan 2016 | Online Presentations | Contributor(s): kaimin Cai
Polymeric micelle is one of the most widely used drug delivery nanomedicine platforms; however, micelle drug delivery systems usually have very low drug loading and poorly defined composition, which greatly limited its further clinical translation. In the course of developing trigger responsive camptothecin conjugates, we discovered an unprecedented approach to prepare core-shell structured drug encapsulates. The polymeric nanoparticles have extremely high drug loading, quantitative loading...
[Illinois] Stretch Induced Hyperexcitability of Mice Callosal Pathway
26 Jan 2016 | Online Presentations | Contributor(s): Anthony Fan
Memory and learning are thought to result from changes in synaptic strength. Previous studies on synaptic physiology in brain slices have traditionally been focused on biochemical processes. Here, we demonstrate with experiments on mouse brain slices that central nervous system plasticity is also sensitive to mechanical stretch. This is important, given the host of clinical conditions involving changes in mechanical tension on the brain, and the normal role that mechanical tension plays in...
[Illinois] Microchip system for multiplexed detection of foodborne pathogens
18 Dec 2015 | Online Presentations | Contributor(s): Carlos Eduardo Duarte-Guevara
Carlos is a Ph.D. candidate at the University of Illinois at Urbana-Champaign, where he is studying label-free electronic biosensors, performing bacteria detection assays, and developing protocols for food sample analysis.
[Illinois] Biophysics 401 Lecture 26: Semester Recap
14 Dec 2015 | Online Presentations | Contributor(s): Paul R Selvin
[Illinois] Biophysics 401 Lecture 25: Cool High Resolution Techniques
11 Dec 2015 | Online Presentations | Contributor(s): Paul R Selvin
[Illinois] Molecular modeling of structure and salt-responsive morphology of polyelectrolyte-based materials
11 Dec 2015 | Online Presentations | Contributor(s): Yaroslava G Yingling
In this talk, I will illustrate our recent progress in prediction of responsive morphologies of polyelectrolytes on the example of DNA- based materials. we used atomistic molecular dynamics simulations to determine the sequence, length, and solvent contributions on the persistence length of ssDNA. Our methodology permitted us to construct a morphological diagram of polyelectrolyte block copolymers in aqueous solution and evaluate the size of aggregates obtained along with their scaling relation
[Illinois] Biophysics 401 Lecture 24: Ion Channels III
10 Dec 2015 | Online Presentations | Contributor(s): Paul R Selvin
[Illinois] Biophysics 401 Lecture 23: Ion Channels II
07 Dec 2015 | Online Presentations | Contributor(s): Paul R Selvin
[Illinois] Biophysics 401 Lecture 22: Ion Channels I
03 Dec 2015 | Online Presentations | Contributor(s): Paul R Selvin