From aaulia@sciences.sdsu.edu Sat Feb 2 16:46:04 2008 From: aaulia@sciences.sdsu.edu (aaulia@sciences.sdsu.edu) Date: Sat, 2 Feb 2008 11:46:04 -0500 Subject: [compsci] COLLOQUIUM: WHEN THE MOLECULES GET TOO BIG, THERE'S ALWAYS HYDROGEN Message-ID: <380-2200826216464967@M2W017.mail2web.com> Title: WHEN THE MOLECULES GET TOO BIG, THERE'S ALWAYS HYDROGEN Date: Friday, February 8th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Andrew L. Cooksey Associate Professor Department of Chemistry San Diego State University Abstract: Hydrogen bonding plays a critical role in the structure and dynamics of many molecular systems, and presents accompanying challenges to the computational chemistry. We've been studying hydrogen bonding in two electron-rich molecular systems: a new organometallic catalyst and the pheophytin cofactor in photosynthesis. Adequate modeling of the hydrogen bond in the catalyst was achieved only by a full quantum mechanical treatment, employing density functional theory, with relatively large basis set. In pheophytin, it appears that explicit treatment of the proton's vibrational wave function within the hydrogen bond may account for a small but significant contribution to an irreversible charge transfer step crucial to photosynthesis. Host: John J. Love 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 -------------------------------------------------------------------- myhosting.com - Premium Microsoft® Windows® and Linux web and application hosting - http://link.myhosting.com/myhosting From aaulia@sciences.sdsu.edu Wed Feb 6 17:04:10 2008 From: aaulia@sciences.sdsu.edu (aaulia@sciences.sdsu.edu) Date: Wed, 6 Feb 2008 12:04:10 -0500 Subject: [compsci] *Reminder* COLLOQUIUM: WHEN THE MOLECULES GET TOO BIG, THERE'S ALWAYS HYDROGEN Message-ID: <380-2200823617410478@M2W013.mail2web.com> Title: WHEN THE MOLECULES GET TOO BIG, THERE'S ALWAYS HYDROGEN Date: Friday, February 8th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Andrew L. Cooksey Associate Professor Department of Chemistry San Diego State University Abstract: Hydrogen bonding plays a critical role in the structure and dynamics of many molecular systems, and presents accompanying challenges to the computational chemistry. We've been studying hydrogen bonding in two electron-rich molecular systems: a new organometallic catalyst and the pheophytin cofactor in photosynthesis. Adequate modeling of the hydrogen bond in the catalyst was achieved only by a full quantum mechanical treatment, employing density functional theory, with relatively large basis set. In pheophytin, it appears that explicit treatment of the proton's vibrational wave function within the hydrogen bond may account for a small but significant contribution to an irreversible charge transfer step crucial to photosynthesis. Host: John J. Love 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 -------------------------------------------------------------------- mail2web.com - Microsoft® Exchange solutions from a leading provider - http://link.mail2web.com/Business/Exchange From aaulia@sciences.sdsu.edu Sun Feb 10 15:41:49 2008 From: aaulia@sciences.sdsu.edu (aaulia@sciences.sdsu.edu) Date: Sun, 10 Feb 2008 10:41:49 -0500 Subject: [compsci] COLLOQUIUM: NOVEL APPLICATION OF POSITIONAL WEIGHT MATRICES FOR TRANSCRIPTION FACTOR BINDING SITE DISCOVERY Message-ID: <380-220082010154149891@M2W028.mail2web.com> Title: NOVEL APPLICATION OF POSITIONAL WEIGHT MATRICES FOR TRANSCRIPTION FACTOR BINDING SITE DISCOVERY Date: Friday, February 15th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Scott Kelley Assistant Professor Department of Biology San Diego State University Abstract: The characterization and interaction of transcriptional regulatory elements is fundamental to understanding how eukaryotic gene networks operate. Identification of the underlying transcription factors (TFs) and their target sequences is crucial to characterizing these regulatory elements. Many computational methods developed to locate TF binding sites (TFBS) have relied on information from previously characterized sites. Yet, the majority of TFs do have not binding site profiles, suggesting these methods may not find uncharacterized sites. We propose a new approach to identify TFs in a set of unaligned sequences with no prior binding site information and with an emphasis on discovering new functional binding sites. Our method compiles positional weight matrices from a set of regulatory sequences taken from co-regulated or tissue-specific genes. These matrices are then used to find statistically over-represented motifs in the input sequences, relative to the rest of the organism's intergenic genome. We test our approach on a set of well-characterized Drosophila development genes. Our results indicate this method effectively predicts known binding sites and also identifies DNA regions that contain promising TFBS candidates. Host: Paul Paolini 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 -------------------------------------------------------------------- mail2web.com – Enhanced email for the mobile individual based on Microsoft® Exchange - http://link.mail2web.com/Personal/EnhancedEmail From aaulia@sciences.sdsu.edu Wed Feb 13 18:30:44 2008 From: aaulia@sciences.sdsu.edu (aaulia@sciences.sdsu.edu) Date: Wed, 13 Feb 2008 13:30:44 -0500 Subject: [compsci] *Reminder* COLLOQUIUM: NOVEL APPLICATION OF POSITIONAL WEIGHT MATRICES FOR TRANSCRIPTION FACTOR BINDING SITE DISCOVERY Message-ID: <380-220082313183044974@M2W027.mail2web.com> Title: NOVEL APPLICATION OF POSITIONAL WEIGHT MATRICES FOR TRANSCRIPTION FACTOR BINDING SITE DISCOVERY Date: Friday, February 15th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Scott Kelley Assistant Professor Department of Biology San Diego State University Abstract: The characterization and interaction of transcriptional regulatory elements is fundamental to understanding how eukaryotic gene networks operate. Identification of the underlying transcription factors (TFs) and their target sequences is crucial to characterizing these regulatory elements. Many computational methods developed to locate TF binding sites (TFBS) have relied on information from previously characterized sites. Yet, the majority of TFs do have not binding site profiles, suggesting these methods may not find uncharacterized sites. We propose a new approach to identify TFs in a set of unaligned sequences with no prior binding site information and with an emphasis on discovering new functional binding sites. Our method compiles positional weight matrices from a set of regulatory sequences taken from co-regulated or tissue-specific genes. These matrices are then used to find statistically over-represented motifs in the input sequences, relative to the rest of the organism's intergenic genome. We test our approach on a set of well-characterized Drosophila development genes. Our results indicate this method effectively predicts known binding sites and also identifies DNA regions that contain promising TFBS candidates. Host: Paul Paolini 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 -------------------------------------------------------------------- mail2web LIVE – Free email based on Microsoft® Exchange technology - http://link.mail2web.com/LIVE From aaulia@sciences.sdsu.edu Sat Feb 16 03:47:29 2008 From: aaulia@sciences.sdsu.edu (aaulia@sciences.sdsu.edu) Date: Fri, 15 Feb 2008 22:47:29 -0500 Subject: [compsci] COLLOQUIUM: BIOPHYSICAL STUDIES OF VIRUS PARTICLES AND THEIR MATURATION: INSIGHTS INTO ELEGANTLY PROGRAMMED NANOMACHINES Message-ID: <380-22008261634729386@M2W042.mail2web.com> Title: BIOPHYSICAL STUDIES OF VIRUS PARTICLES AND THEIR MATURATION: INSIGHTS INTO ELEGANTLY PROGRAMMED NANOMACHINES Date: Friday, February 22nd, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: John E. Johnson Professor, Department of Molecular Biology The Scripps Research Institute Abstract: Complex virus particles such as HIV, Herpes Viruses and dsDNA bacteriophages are programmed nanomachines that assemble in a fragile shell that matures through a series of intermediates to form an infectious, robust particle. We have analyzed mature bacteriophage and intermediates in maturation, defining the biophysical and mathematical nature of the transitions and their driving forces. Through chemistry and physics, these particles shape an energy landscape resulting in a series of exothermic transitions and a final maturation that relies on a Brownian ratchet. The presentation will describe the synthesis of structural and other biophysical data that leads to an understanding of emergent biological behavior in terms of physics and chemistry. Host: Joe Mahaffy 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 -------------------------------------------------------------------- mail2web.com - Microsoft® Exchange solutions from a leading provider - http://link.mail2web.com/Business/Exchange From aaulia@sciences.sdsu.edu Wed Feb 20 18:06:26 2008 From: aaulia@sciences.sdsu.edu (aaulia@sciences.sdsu.edu) Date: Wed, 20 Feb 2008 13:06:26 -0500 Subject: [compsci] *Reminder* COLLOQUIUM: BIOPHYSICAL STUDIES OF VIRUS PARTICLES AND THEIR MATURATION: INSIGHTS INTO ELEGANTLY PROGRAMMED NANOMACHINES Message-ID: <380-22008232018626346@M2W006.mail2web.com> Title: BIOPHYSICAL STUDIES OF VIRUS PARTICLES AND THEIR MATURATION: INSIGHTS INTO ELEGANTLY PROGRAMMED NANOMACHINES Date: Friday, February 22nd, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: John E. Johnson Professor, Department of Molecular Biology The Scripps Research Institute Abstract: Complex virus particles such as HIV, Herpes Viruses and dsDNA bacteriophages are programmed nanomachines that assemble in a fragile shell that matures through a series of intermediates to form an infectious, robust particle. We have analyzed mature bacteriophage and intermediates in maturation, defining the biophysical and mathematical nature of the transitions and their driving forces. Through chemistry and physics, these particles shape an energy landscape resulting in a series of exothermic transitions and a final maturation that relies on a Brownian ratchet. The presentation will describe the synthesis of structural and other biophysical data that leads to an understanding of emergent biological behavior in terms of physics and chemistry. Host: Joe Mahaffy Co-Host: Roland Wolkowicz 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 -------------------------------------------------------------------- myhosting.com - Premium Microsoft® Windows® and Linux web and application hosting - http://link.myhosting.com/myhosting From aaulia@sciences.sdsu.edu Mon Feb 25 03:22:59 2008 From: aaulia@sciences.sdsu.edu (aaulia@sciences.sdsu.edu) Date: Sun, 24 Feb 2008 22:22:59 -0500 Subject: [compsci] COLLOQUIUM: NOISE REMOVAL AND STRUCTURE ENHANCEMENT FOR ELECTRON TOMOGRAPHY OF MITOCHONDRIA Message-ID: <380-22008212532259191@M2W016.mail2web.com> ************************************************** IN CELEBRATION OF GENE GOLUB'S LIFE Gene Golub (February 29, 1932 - November 16, 2007) Following this special colloquium, please join us at SDSU campus pub, Monty's, to celebrate Gene's life and accomplishments. This is a special place, as it is where we enjoyed spending time with him when he visited SDSU. ************************************************** Title: NOISE REMOVAL AND STRUCTURE ENHANCEMENT FOR ELECTRON TOMOGRAPHY OF MITOCHONDRIA Date: Friday, February 29th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Peter Blomgren Department of Mathematics and Statistics San Diego State University Abstract: We review some recent progress in image enhancement aimed at improving mitochondrial images obtained from electron tomography. We propose: (*) an iterative method, based on the well established total variation (TV) approach to image processing, whereby we can obtain a good approximation to the true image, with minimum human intervention; (*) a new image smoothing and edge detection technique that employs a combination of nonlinear diffusion and bilateral filtering. [Joint work with Carlos Bazan] 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 -------------------------------------------------------------------- mail2web LIVE – Free email based on Microsoft® Exchange technology - http://link.mail2web.com/LIVE From aaulia@sciences.sdsu.edu Wed Feb 27 17:55:26 2008 From: aaulia@sciences.sdsu.edu (aaulia@sciences.sdsu.edu) Date: Wed, 27 Feb 2008 12:55:26 -0500 Subject: [CSRC SDSU] *Reminder* COLLOQUIUM: NOISE REMOVAL AND STRUCTURE ENHANCEMENT FOR ELECTRON TOMOGRAPHY OF MITOCHONDRIA Message-ID: <380-220082327175526517@M2W024.mail2web.com> ************************************************** IN CELEBRATION OF GENE GOLUB'S LIFE Gene Golub (February 29, 1932 - November 16, 2007) Following this special colloquium, please join us at SDSU campus pub, Monty's, to celebrate Gene's life and accomplishments. This is a special place, as it is where we enjoyed spending time with him when he visited SDSU. ************************************************** Title: NOISE REMOVAL AND STRUCTURE ENHANCEMENT FOR ELECTRON TOMOGRAPHY OF MITOCHONDRIA Date: Friday, February 29th, 2008 Time: 3:30 pm Location: GMCS 214 Speaker: Peter Blomgren Department of Mathematics and Statistics San Diego State University Abstract: We review some recent progress in image enhancement aimed at improving mitochondrial images obtained from electron tomography. We propose: (*) an iterative method, based on the well established total variation (TV) approach to image processing, whereby we can obtain a good approximation to the true image, with minimum human intervention; (*) a new image smoothing and edge detection technique that employs a combination of nonlinear diffusion and bilateral filtering. [Joint work with Carlos Bazan] 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 -------------------------------------------------------------------- mail2web.com – Enhanced email for the mobile individual based on Microsoft® Exchange - http://link.mail2web.com/Personal/EnhancedEmail