Preliminary Program subject to change
21018 Computational Biology: Systems Modeling II
OverviewThis session is devoted to new developments in the theoretical and computational studies of biological systems. Such systems include protein/DNA interactions, protein/protein interactions, genetic networks, metabolic pathways, signal transduction pathways and inter- or intra-cellular transport of biomolecules. Presentations will focus on theoretical and computational techniques to predict, engineer or analyze the kinetic and thermodynamic properties of these systems. Emphasis will be placed on techniques that enable engineering by connecting molecular-level to macroscopic system-level properties. Additional favored topics include: new biological insights from studies of systems and industrial applications of computationally-driven biological systems engineering. Validation through comparison with experimental results is strongly encouraged.
Primary SponsorComputational Molecular Science and Engineering Forum (21)
Co-Sponsor(s)Engineering Fundamentals in Life Science (15d)

Chair

Vassily Hatzimanikatis
Chemical and Biological Engineering
Northwestern University
2145 Sheridan Rd.
Evanston, IL 60208
Phone Number: 847-491-5357
Email: vassily@northwestern.edu

CoChair

David Klinke
Assistant Professor
Department of Chemical Engineering
West Virginia University
P.O. Box 6102
Morgantown, WV 26506-6102
Phone Number: 304-293-2111 ext 2432
Fax Number: 304-293-4139
Email: david.klinke@mail.wvu.edu
Characterizing the Interval Timer within Drosophila's Circadian Clock
Robert S. Kuczenski1, Kevin C. Hong1, Jordi García-Ojalvo2 and Kelvin H. Lee1, (1)School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853-5201, (2)Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Colom 11, E-08222 Terrassa, Barcelona, Spain
Analyzing Individual Cancer Cell Motility with Chemotaxis Perspective
Alka A. Potdar and Peter T. Cummings, Chemical engineering, Vanderbilt University, 107 Olin Hall, 24th & Garland Avenues, Nashville, TN 37235
A Combined Modeling and Experimental Approach for in Vivo Parameter Estimation
Gregory T. Reeves and Stas Shvartsman, Department of Chemical Engineering and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
Characterization of Cross-Hybridization Via Stochastic Simulation
Erdem Arslan, Chemical Engineering, Lehigh University, 111 Research Drive, Bethlehem, PA 18015 and Ian J. Laurenzi, Chemical Engineering, Lehigh University, B330 Iacocca Hall, 111 Research Dr., Bethlehem, PA 18015
Improved Logical Formulation for Transcription Regulatory Networks Reconstruction Via Integer Linear Programming
Joao Natali and Jose M. Pinto, Othmer-Jacobs Department of Chemical and Biological Engineering, Polytechnic University, Six Metrotech Center, Brooklyn, NY 11201
Deterministic and Stochastic Modeling of Genetic Networks with Positive Feedback Architecture
Michail Stamatakis, Chemical and Biomolecular Engineering Department, Rice University, Houston, TX 77005 and Nikos Mantzaris, Chemical and Biomolecular Engineering, Rice University, Houston, TX 77005
Modeling Ire1p Regulation and Activation in the Yeast Upr
Scott Hildebrandt1, David Raden2, Anne Skaja Robinson2 and Francis J. Doyle III3, (1)Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, (2)University of Delaware, 259 Colburn Laboratory, Department of Chemical Engineering, Newark, DE 19716, (3)Chemical Engineering/Biomolecular Science and Engineering Program, University of California Santa Barbara, UCSB, Santa Barbara, CA 93106-5080
Adhesive Dynamics Simulations of the Shear Threshold Effect for Leukocytes
Kelly E. Caputo, Chemical and Biomolecular Engineering, University of Pennsylvania, 220 South 33rd St., 311A Towne Building, Philadelphia, PA 19104 and Daniel A. Hammer, University of Pennsylvania, Department of Bioengineering, 120 Hayden Hall, 3320 Smith Walk, Philadelphia, PA 19104
Molecular Mechanisms of HIV-1 Latency: Stochastics in Gene Expression and Chromatin Regulation
John C. Burnett, Chemical Engineering, University of California at Berkeley, Department of Chemical Engineering, 201 Gilman Hall, Berkeley, CA 94720-1462, Adam P. Arkin, Bioengineering, University of California at Berkeley, Department of Chemical Engineering, 201 Gilman Hall, Berkeley, CA 94720-1462 and David V. Schaffer, Chemical Engineering, University of California, Berkeley, 201 Gilman Hall, Berkeley, CA 94707

Computational Molecular Science and Engineering Forum