From aaulia@sciences.sdsu.edu Wed Apr 2 23:58:39 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Wed, 2 Apr 2008 15:58:39 -0700 Subject: [CSRC SDSU] *Reminder* COLLOQUIUM: FORMULATION OF A TARGET-MATRIX PARADIGM FOR MESH OPTIMIZATION Message-ID: ------=_Part_4330_5592668.1207177119870 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Title: FORMULATION OF A TARGET-MATRIX PARADIGM FOR MESH OPTIMIZATION Date: Friday, April 4th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Patrick M. Knupp Optimization and Uncertainty Estimation Dept. Sandia National Laboratories Abstract: PDE simulations generally require a mesh on which the physical domain is discretized. The mesh can have a strong impact on solution accuracy & efficiency if not constructed properly. Methods to address this issue include solution-adaptive meshes, smoothing & swapping, and mesh optimization. An extension of Direct optimization (Castillo & others) will be described in this talk. A Target-Matrix paradigm (TMP) for improving mesh quality by node repositioning via optimization is formulated in which target matrices describe the desired Jacobian matrix at mesh sample points. Attention is devoted to basic definitions & properties of mesh-based matrices, local & non-local quality metrics, and objective functions based on the power-mean. New local metrics are proposed that satisfy seven important requirements for a properly formulated mesh quality metric. Numerical experiments illustrate the theoretical properties and indicate the potential of this paradigm. Host: Jose Castillo For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu ------=_Part_4330_5592668.1207177119870 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Title: FORMULATION OF A TARGET-MATRIX PARADIGM FOR MESH OPTIMIZATION

Date: Friday, April 4th, 2008
Time: 3:30 pm
Location: GMCS 214


Speaker:

Patrick M. Knupp
Optimization and Uncertainty Estimation Dept.
Sandia National Laboratories


Abstract:

PDE simulations generally require a mesh on which the physical
domain is discretized.  The mesh can have a strong impact on
solution accuracy & efficiency if not constructed properly.
Methods to address this issue include solution-adaptive meshes,
smoothing & swapping, and mesh optimization.  An extension of
Direct optimization (Castillo & others) will be described in
this talk.

A Target-Matrix paradigm (TMP) for improving mesh quality by
node repositioning via optimization is formulated in which
target matrices describe the desired Jacobian matrix at mesh
sample points.  Attention is devoted to basic definitions &
properties of mesh-based matrices, local & non-local quality
metrics, and objective functions based on the power-mean.
New local metrics are proposed that satisfy seven important
requirements for a properly formulated mesh quality metric.
Numerical experiments illustrate the theoretical properties
and indicate the potential of this paradigm.


Host: Jose Castillo

For future events, please visit our web site at:
http://www.csrc.sdsu.edu/csrc/events/colloquium/

******************************
*************
Akmal Aulia
PhD Student
Computational Science Research Center
San Diego State University
Phone: 619-335-7187
Email: aaulia@sciences.sdsu.edu


------=_Part_4330_5592668.1207177119870-- From aaulia@sciences.sdsu.edu Thu Apr 3 05:16:43 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Wed, 2 Apr 2008 21:16:43 -0700 (PDT) Subject: [CSRC SDSU] *Reminder* COLLOQUIUM: FORMULATION OF A TARGET-MATRIX PARADIGM FOR MESH OPTIMIZATION Message-ID: Title: FORMULATION OF A TARGET-MATRIX PARADIGM FOR MESH OPTIMIZATION Date: Friday, April 4th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Patrick M. Knupp Optimization and Uncertainty Estimation Dept. Sandia National Laboratories Abstract: PDE simulations generally require a mesh on which the physical domain is discretized. The mesh can have a strong impact on solution accuracy & efficiency if not constructed properly. Methods to address this issue include solution-adaptive meshes, smoothing & swapping, and mesh optimization. An extension of Direct optimization (Castillo & others) will be described in this talk. A Target-Matrix paradigm (TMP) for improving mesh quality by node repositioning via optimization is formulated in which target matrices describe the desired Jacobian matrix at mesh sample points. Attention is devoted to basic definitions & properties of mesh-based matrices, local & non-local quality metrics, and objective functions based on the power-mean. New local metrics are proposed that satisfy seven important requirements for a properly formulated mesh quality metric. Numerical experiments illustrate the theoretical properties and indicate the potential of this paradigm. Host: Jose Castillo For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu From aaulia@sciences.sdsu.edu Sat Apr 5 00:15:51 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Fri, 4 Apr 2008 16:15:51 -0700 (PDT) Subject: [CSRC SDSU] COLLOQUIUM: DOES MOLECULAR MOTION MATTER FOR PROTEIN FUNCTION? Message-ID: Title: DOES MOLECULAR MOTION MATTER FOR PROTEIN FUNCTION? Date: Friday, April 11th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: John J. Love Department of Chemistry and Biochemistry San Diego State University Abstract: The correlation between protein structure and function is well established yet the role flexibility/stability plays in protein function is still being explored. In the Love laboratory we employ protein design methodologies to explore (and measure) the correlation between flexibility/stability and protein function. Overall we use computational and experimental approaches to explore three related areas in the field of protein design: 1) The role intrinsic flexibility/stability plays in protein function. 2) Methods and screens designed to increase the intrinsic stability of proteins. 3) The de novo design of novel protein/protein interactions. For the project in which we are exploring the role flexibility/stability plays in protein function we are utilizing a well-characterized protein/DNA interaction (i.e., the LEF-1 HMG domain bound to cognate DNA). NMR analysis of the LEF-1 DNA binding domain in complex with DNA revealed that the protein is quite well-ordered while bound to its consensus sequence. On the other hand the free LEF-1 domain exhibits considerable structural instability and conformational heterogeneity. This behavior raises the following questions: Why does the free DNA binding domain exhibit such significant disorder? Could the flexibility be necessary for the gross perturbations that occur within the DNA upon binding? Is this behavior functionally essential for DNA bending? What impact would the introduction of stability have on the protein.s function? For that matter, is it possible to introduce stability? These questions, along with our attempts to answer them will be described. In addition to the above I will also describe our ongoing efforts to develop in vivo screens for protein stability using rational design in combination with computational methods. Finally I will discuss our goal of using computational and experimental methods to engineer proteins that bind and inactivate important physiological targets. Host: Andrew Cooksy For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu From aaulia@sciences.sdsu.edu Wed Apr 9 23:20:29 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Wed, 9 Apr 2008 15:20:29 -0700 (PDT) Subject: [CSRC SDSU] *Reminder* COLLOQUIUM: DOES MOLECULAR MOTION MATTER FOR PROTEIN FUNCTION? Message-ID: Title: DOES MOLECULAR MOTION MATTER FOR PROTEIN FUNCTION? Date: Friday, April 11th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: John J. Love Department of Chemistry and Biochemistry San Diego State University Abstract: The correlation between protein structure and function is well established yet the role flexibility/stability plays in protein function is still being explored. In the Love laboratory we employ protein design methodologies to explore (and measure) the correlation between flexibility/stability and protein function. Overall we use computational and experimental approaches to explore three related areas in the field of protein design: 1) The role intrinsic flexibility/stability plays in protein function. 2) Methods and screens designed to increase the intrinsic stability of proteins. 3) The de novo design of novel protein/protein interactions. For the project in which we are exploring the role flexibility/stability plays in protein function we are utilizing a well-characterized protein/DNA interaction (i.e., the LEF-1 HMG domain bound to cognate DNA). NMR analysis of the LEF-1 DNA binding domain in complex with DNA revealed that the protein is quite well-ordered while bound to its consensus sequence. On the other hand the free LEF-1 domain exhibits considerable structural instability and conformational heterogeneity. This behavior raises the following questions: Why does the free DNA binding domain exhibit such significant disorder? Could the flexibility be necessary for the gross perturbations that occur within the DNA upon binding? Is this behavior functionally essential for DNA bending? What impact would the introduction of stability have on the protein.s function? For that matter, is it possible to introduce stability? These questions, along with our attempts to answer them will be described. In addition to the above I will also describe our ongoing efforts to develop in vivo screens for protein stability using rational design in combination with computational methods. Finally I will discuss our goal of using computational and experimental methods to engineer proteins that bind and inactivate important physiological targets. Host: Andrew Cooksy For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu ******************************************* From aaulia@sciences.sdsu.edu Mon Apr 14 08:09:27 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Mon, 14 Apr 2008 00:09:27 -0700 (PDT) Subject: [CSRC SDSU] COLLOQUIUM: ENERGY CASCADE IN TURBULENT FLOWS; QUANTIFYING EFFECTS OF LOCAL AND NONLOCAL INTERACTIONS Message-ID: Title: ENERGY CASCADE IN TURBULENT FLOWS; QUANTIFYING EFFECTS OF LOCAL AND NONLOCAL INTERACTIONS Date: Friday, April 18th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Julian Andrzej Domaradzki Aerospace and Mechanical Engineering University of Southern California Abstract: The classical Kolmogorov theory of turbulence is based on the concept of the energy transfer from larger to progressively smaller scales of motion. The theory assumes that bulk of the energy transfer in the inertial range of turbulence occurs between scales of similar size, a process known as the local energy cascade. The assumed locality allows to postulate that after multiple cascade steps the small scale dynamics become universal, i.e., independent of particulars of large scales that are determined by geometry, boundary conditions, and forces causing a particular flow. Yet despite its central role in the Kolmogorov theory the locality assumption cannot be easily verified, neither analytically nor experimentally. This is because, mathematically, the energy transfer is a result of interactions among different scales of motion originating from the nonlinear term in the Navier-Stokes equation that couples all scales. Relevant questions can be productively addressed using databases generated in large scale numerical simulations. We describe such databases and use them to compute detailed energy exchanges between scales of motion with well defined sizes, obtained by decomposing numerical velocity fields using banded filters, and investigate how the detailed transfers contribute to the global quantities such as the classical energy transfer and the energy flux. The developed procedure allows to quantify locality of the energy transfer and to address a persistent controversy concerning the role of nonlocal interactions in this process, i.e., of much larger scales than those transferring energy. The analysis of detailed interactions reveals that the individual nonlocal contributions are always large but significant cancellations lead to the global quantities asymptotically dominated by the local interactions. Apart from an intellectual challenge of clarifying these issues, obtained results have bearing on practical questions of turbulence modeling that will be addressed in the talk. Host: Gustaaf Jacobs For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu ******************************************* From aaulia@sciences.sdsu.edu Thu Apr 17 00:05:01 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Wed, 16 Apr 2008 16:05:01 -0700 (PDT) Subject: [CSRC SDSU] *Reminder* COLLOQUIUM: ENERGY CASCADE IN TURBULENT FLOWS; QUANTIFYING EFFECTS OF LOCAL AND NONLOCAL INTERACTIONS Message-ID: Title: ENERGY CASCADE IN TURBULENT FLOWS; QUANTIFYING EFFECTS OF LOCAL AND NONLOCAL INTERACTIONS Date: Friday, April 18th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Julian Andrzej Domaradzki Aerospace and Mechanical Engineering University of Southern California Abstract: The classical Kolmogorov theory of turbulence is based on the concept of the energy transfer from larger to progressively smaller scales of motion. The theory assumes that bulk of the energy transfer in the inertial range of turbulence occurs between scales of similar size, a process known as the local energy cascade. The assumed locality allows to postulate that after multiple cascade steps the small scale dynamics become universal, i.e., independent of particulars of large scales that are determined by geometry, boundary conditions, and forces causing a particular flow. Yet despite its central role in the Kolmogorov theory the locality assumption cannot be easily verified, neither analytically nor experimentally. This is because, mathematically, the energy transfer is a result of interactions among different scales of motion originating from the nonlinear term in the Navier-Stokes equation that couples all scales. Relevant questions can be productively addressed using databases generated in large scale numerical simulations. We describe such databases and use them to compute detailed energy exchanges between scales of motion with well defined sizes, obtained by decomposing numerical velocity fields using banded filters, and investigate how the detailed transfers contribute to the global quantities such as the classical energy transfer and the energy flux. The developed procedure allows to quantify locality of the energy transfer and to address a persistent controversy concerning the role of nonlocal interactions in this process, i.e., of much larger scales than those transferring energy. The analysis of detailed interactions reveals that the individual nonlocal contributions are always large but significant cancellations lead to the global quantities asymptotically dominated by the local interactions. Apart from an intellectual challenge of clarifying these issues, obtained results have bearing on practical questions of turbulence modeling that will be addressed in the talk. Host: Gustaaf Jacobs For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu ******************************************* From aaulia@sciences.sdsu.edu Fri Apr 18 23:55:43 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Fri, 18 Apr 2008 15:55:43 -0700 (PDT) Subject: [CSRC SDSU] PhD DISSERTATION DEFENSE: COMPUTATIONAL MODELING AND BIFURCATION ANALYSIS OF BUBBLING FLUIDIZED PROCESSES Message-ID: *This upcoming talk is a PhD Dissertation Defense* Title: COMPUTATIONAL MODELING AND BIFURCATION ANALYSIS OF BUBBLING FLUIDIZED PROCESSES Date: Friday, April 25th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Bing Zhu PhD in Computational Science San Diego State University Abstract: Fluidization processes have many important applications in industry, in particular, in chemical, fossil, and petrochemical industries where good gas-solid mixing is required. Such mixing is commonly achieved through bubbles which are formed spontaneously and whose time-evolution appears to be governed by low-dimensional deterministic dynamics. Understanding the space and time dynamics in more detail is critical to future development of technologies that rely on the fluidization phenomenon---transport of solid particles by fluids---such as chemical reactors. In response to this need, we use a low-dimensional, computational agent-based bubble model to study the changes in the global bubble dynamics in response to changes in the frequency of the rising bubbles. A computationally-based bifurcation analysis shows that the collective bubble dynamics undergoes a series of transitions from equilibrium points to highly periodic orbits, chaotic attractors, and even intermittent behavior between periodic orbits and chaotic sets. Using ideas and methods from nonlinear dynamics and time-series analysis, we are able to approximate nonlinear models that allow for long-term predictions and the possibility of developing control algorithms. Additionally, we employ the Proper Orthogonal Decomposition to better understand the bubble dynamics generated by multiple injectors. -This is a joint project with the Chaos Group at Oak Ridge National Laboratory- Advisors: Antonio Palacios and Peter Blomgren For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu ******************************************* From aaulia@sciences.sdsu.edu Tue Apr 22 18:47:46 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Tue, 22 Apr 2008 10:47:46 -0700 (PDT) Subject: [CSRC SDSU] COLLOQUIUM: TEN MIRANDEAN PRINCIPLES FOR TEACHING, LEARNING AND CREATING MATH Message-ID: Title: TEN MIRANDEAN PRINCIPLES FOR TEACHING, LEARNING AND CREATING MATH Date: Monday, April 28th, 2008 Time: 2:00 pm - 3:50 pm Location: GMCS 328 Speaker: Guillermo Miranda Universidad Central de Venezuela Abstract: A long teaching and research experience has led the author to synthetize into 10 simple guiding rules, called "Mirandean Principles", the ways used by mathematicians (often unconsciously ) to formulate definitions, theories and problems, as well as to motivate the how to solve the questions posed. In this talk, a number of elementary mathematical questions are illuminated from this point of view, exemplifying the use of one or several of these 10 principles. Even humanistically minded persons can get a true understanding of theorems or procedures, which, otherwise, would remain ither abstruse or mechanically memorized. The 10 Principles are: 1) Interpret Definitions and Theorems as a "stage play". 2) Change of Plane or Dimension, 3) Creation by "baptizing", 4) Change everything so that everything stays the same, 5) Change point of view and look for the most convenient perspective, 6) "Walk around" obstructions or difficulties, 7) The totality is the sum ( or union ) of the parts, 8) Search for the new unknown at the old known or in the boundaries ( or limit ) of the old known, 9) Analysis and Synthesis ( Motivation for the defining integrals, fluxes, etc. ), 10) Use curved mirrors to illustrate isomorphisms between mathematical structures apparently different. For example, different matrix representations of a single linear transformation, or positive real numbers under multiplication and real numbers under addition via Logarithms ). Systematic use of these tools starting with kids and also in the first semesters for undergraduates would enhance their mathematical ability as well as their performance where math is used, as in physics or chemistry. Host: Jose E. Castillo For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu ******************************************* From aaulia@sciences.sdsu.edu Tue Apr 22 18:58:00 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Tue, 22 Apr 2008 10:58:00 -0700 (PDT) Subject: [CSRC SDSU] [PHYSICS-ASTRONOMY] COLLOQUIUM: LIGHT AND GRAVITY; A THEORY OF VECTOR GRAVITATIONAL WAVES INDEPENDET OF EINSTEIN'S GENERAL THEORY, DEVELOPING EARLIER IDEAS OF LORENTZ, COMPTON AND WHEELER, AND INTRODUCING THE NEW COSMOGONIC CONCEPT OF TRIO-HOLES. Message-ID: Title: LIGHT AND GRAVITY: A THEORY OF VECTOR GRAVITATIONAL WAVES INDEPENDET OF EINSTEIN'S GENERAL THEORY, DEVELOPING EARLIER IDEAS OF LORENTZ, COMPTON AND WHEELER, AND INTRODUCING THE NEW COSMOGONIC CONCEPT OF TRIO-HOLES. Date: Friday, April 25th, 2008 Time: 2:00 PM Location: P-148 (refreshments will be served at 1:45 PM in P145A) Speaker: Guillermo Miranda Universidad Central de Venezuela Abstract: In contrast with the Einstein-Dirac gravitational waves obtained under many simplifying assumptions, in this work exact vector gravitational waves are obtained as solutions of a linear system of PDEs formally analogous to the Maxwellian system for the electric and magnetic fields. With these linear equations, the precession of Mercury's perihelium and other celestial phenomena are easily explained (Now have a Gravitational Larmor's Theorem, and also a gravitomagnetic force that accounts for nebular angular momentum etc.). Gravitomagnetic fields are postulated not only as generated by matter in motion, as Wheeler (and also Faraday) thought, but also through intense light photonic beams converging in a concentration point or "trio-hole" prior to the Big Bang, with partial reflection, process that can be easily modelled under the Maxwell-Lorentz framework.http://www.physics.sdsu.edu/seminars/ *Funded in part from SDSU student's instructionally related activity fees. *Hosting by the SDSU Department of Physics and Department of Astronomy* From aaulia@sciences.sdsu.edu Tue Apr 22 19:04:23 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Tue, 22 Apr 2008 11:04:23 -0700 (PDT) Subject: [CSRC SDSU] [AEROSPACE] COLLOQUIUM: THE FLIGHTS OF BIRDS, BATS AND OTHER SMALL-SCALE FLYING MACHINES Message-ID: Title: THE FLIGHTS OF BIRDS, BATS AND OTHER SMALL-SCALE FLYING MACHINES Date: Thursday, April 24, 2008 Time: 2 PM Location: EE203 Speaker: G.R. Spedding Department of Aerospace and Mechanical Engineering University of Southern California Abstract: Animal flight has long been of interest to biologists, and now that it is practical to make small-scale flying machines that are about the same size as birds or bats, it has become interesting also to engineers. The aerodynamics at this scale are very complex because the viscous, laminar boundary layer on the wing is very sensitive to small disturbances. For this reason experiments are difficult and frequently unreliable, while numerical simulations are equally difficult and possibly incorrect, achieving stability only through artificial numerical dissipation. This talk will summarise recent experimental results from detailed measurements of fixed wings in a low turbulence wind tunnel and from similar measurements of live, trained birds and bats in flight. We will pay particular attention to the extent to which lessons transfer from one field to the other. Successes and failures both can improve our understanding of natural flight and how to engineer our own devices. Hosting by the SDSU Department of Aerospace Engineering From aaulia@sciences.sdsu.edu Wed Apr 23 16:01:31 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Wed, 23 Apr 2008 08:01:31 -0700 (PDT) Subject: [CSRC SDSU] *Reminder* PhD DISSERTATION DEFENSE: COMPUTATIONAL MODELING AND BIFURCATION ANALYSIS OF BUBBLING FLUIDIZED PROCESSES Message-ID: *This upcoming talk is a PhD Dissertation Defense* Title: COMPUTATIONAL MODELING AND BIFURCATION ANALYSIS OF BUBBLING FLUIDIZED PROCESSES Date: Friday, April 25th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Bing Zhu PhD in Computational Science San Diego State University Abstract: Fluidization processes have many important applications in industry, in particular, in chemical, fossil, and petrochemical industries where good gas-solid mixing is required. Such mixing is commonly achieved through bubbles which are formed spontaneously and whose time-evolution appears to be governed by low-dimensional deterministic dynamics. Understanding the space and time dynamics in more detail is critical to future development of technologies that rely on the fluidization phenomenon---transport of solid particles by fluids---such as chemical reactors. In response to this need, we use a low-dimensional, computational agent-based bubble model to study the changes in the global bubble dynamics in response to changes in the frequency of the rising bubbles. A computationally-based bifurcation analysis shows that the collective bubble dynamics undergoes a series of transitions from equilibrium points to highly periodic orbits, chaotic attractors, and even intermittent behavior between periodic orbits and chaotic sets. Using ideas and methods from nonlinear dynamics and time-series analysis, we are able to approximate nonlinear models that allow for long-term predictions and the possibility of developing control algorithms. Additionally, we employ the Proper Orthogonal Decomposition to better understand the bubble dynamics generated by multiple injectors. -This is a joint project with the Chaos Group at Oak Ridge National Laboratory- Advisors: Antonio Palacios and Peter Blomgren For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu ******************************************* From aaulia@sciences.sdsu.edu Sun Apr 27 19:54:03 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Sun, 27 Apr 2008 11:54:03 -0700 (PDT) Subject: [CSRC SDSU] COLLOQUIUM: AN OVERVIEW OF STATISTICAL METHODS IN cDNA MICROARRAY DATA ANALYSIS Message-ID: Title: AN OVERVIEW OF STATISTICAL METHODS IN cDNA MICROARRAY DATA ANALYSIS Date: Friday, May 2nd, 2008 Time: 3:30 pm - 4:30 pm Location: GMCS 214 Speaker: Chao-Jen Wong Postdoctoral Researcher Computational Science Research Center San Diego State University Abstract: During the last decade, there has been a rapid expansion of knowledge in the fields of computational biology, systems biology, and bioinformatics. A new tool in these exciting new sciences, microarray techniques have emerged and hold a great promise in understanding the underlying biology and function of genomes in a global manner. The challenge of analyzing gene expression data with large dimensionality has led to interdisciplinary investigations between molecular biology and statistics. In this talk, I present (i) an overview of the development of statistical methods in microarray data analysis, particularly empirical Bayes, (ii) the methods for Gene Ontology (GO) and canonical KEGG pathway analysis, and (iii) profiles of the gene expression data obtained from neonatal rat heart cells in response to anti-diabetic rosiglitazone treatment. Host: Jose E. Castillo For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu ******************************************* From aaulia@sciences.sdsu.edu Wed Apr 30 17:57:47 2008 From: aaulia@sciences.sdsu.edu (Akmal Aulia) Date: Wed, 30 Apr 2008 09:57:47 -0700 (PDT) Subject: [CSRC SDSU] *Reminder* COLLOQUIUM: AN OVERVIEW OF STATISTICAL METHODS IN cDNA MICROARRAY DATA ANALYSIS Message-ID: Title: AN OVERVIEW OF STATISTICAL METHODS IN cDNA MICROARRAY DATA ANALYSIS Date: Friday, May 2nd, 2008 Time: 3:30 pm - 4:30 pm Location: GMCS 214 Speaker: Chao-Jen Wong Postdoctoral Researcher Computational Science Research Center San Diego State University Abstract: During the last decade, there has been a rapid expansion of knowledge in the fields of computational biology, systems biology, and bioinformatics. A new tool in these exciting new sciences, microarray techniques have emerged and hold a great promise in understanding the underlying biology and function of genomes in a global manner. The challenge of analyzing gene expression data with large dimensionality has led to interdisciplinary investigations between molecular biology and statistics. In this talk, I present (i) an overview of the development of statistical methods in microarray data analysis, particularly empirical Bayes, (ii) the methods for Gene Ontology (GO) and canonical KEGG pathway analysis, and (iii) profiles of the gene expression data obtained from neonatal rat heart cells in response to anti-diabetic rosiglitazone treatment. Host: Jose E. Castillo For future events, please visit our web site at: http://www.csrc.sdsu.edu/csrc/events/colloquium/ ******************************************* Akmal Aulia PhD Student Computational Science Research Center San Diego State University Phone: 619-335-7187 Email: aaulia@sciences.sdsu.edu *******************************************