Preliminary Program subject to change
21014 Computational Biology: Proteins and DNA
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

Louis A. Clark
Postdoctoral Fellow
Biogen Idec
14 Cambridge ctr
Cambridge, MA 02142
Phone Number: (415) 254-8038
Fax Number: (617) 679-3208
Email: louie@alumni.northwestern.edu

* Membership Number 0090040493

CoChair

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

CoChair

M. Scott Shell
Postdoctoral scholar
Pharmaceutical Chemistry
University of California San Francisco
600 16th Street
Box 2240
San Francisco, CA 94143
Phone Number: 415-476-6875
Fax Number: 415-502-4222
Email: mscottshell@gmail.com
Role of Histone Tails and Linker Histone in Chromatin Folding
Gaurav Arya, Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 31 Washington Place, Room 1021 Main, New York, NY 10003 and Tamar Schlick, New York University, 31 Washington Place, Main 1001, New York, NY 10003
MD(T, F) and Experimental Studies on the Thermomechanical Stability of Three-Helix Bundle Repeats
Vanessa Ortiz1, Colin Johnson2, Michael L. Klein3 and Dennis E. Discher2, (1)Univ.Pennsylvania, 112 Towne Bldg, Philadelphia, PA 19104, (2)Chemical and Biomolecular Engineering, Univ.Pennsylvania, 112 Towne Bldg, Philadelphia, PA 19104, (3)Chemistry, Univ.Pennsylvania, 112 Towne Bldg, Philadelphia, PA 19104
Molecular Dynamics Simulations to Guide the Design of Peptide Antibiotics
Himanshu Khandelia, Chemical Engineering and Materials Science, University of Minnesota, #112, 421, Washington Avenue SE, Minneapolis, MN 55455 and Yiannis N. Kaznessis, Chemical Engineering. and Materials. Science, University of Minnesota, 499, Walter Library, 117, Pleasant St. SE, Minneapolis, MN 55455
Insights into a Model Peptide System - a Polarizable Force Field Molecular Simulation Study
Di Wu and Teresa Head-Gordon, Department of Bioengineering, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
Physics-Based Protein Structure Prediction by Zipping and Assembly
M. Scott Shell1, J. D. Chodera2, S. B. Ozkan1, V. A. Voelz2, A. G. Wu1 and Ken A. Dill3, (1)Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Box 2240, San Francisco, CA 94143, (2)Graduate group in biophysics, University of California San Francisco, 600 16th Street, Box 2240, San Francisco, CA 94143, (3)Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, N-472F, San Francisco, CA 94143
An Improved Coarse Grain Model of DNA and Applications
Thomas A. Knotts IV, Aslin Izmitli and Juan J. De Pablo, Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691
Modulating the DNA Affinity of Elk-1 with Computationally Selected Mutations
Sheldon Park1, Eric T. Boder2 and Jeffery G. Saven1, (1)Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104, (2)University of Pennsylvania, 220 South 33rd Street, Philadelphia, PA 19104
Molecular Dynamics of DNA Translocation through Nanoelectrode Gaps
Xiongce Zhao, Nanomaterials Theory Institute, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, Christina M. Payne, Chemical Engineering, Vanderbilt University, 24th and Garland Ave., 118 Olin Hall, Nashville, TN 37235, Peter T. Cummings, Chemical Engineering, Vanderbilt University, Olin Hall, 24th and Garland, Nashville, TN 37235 and James W. Lee, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831

Computational Molecular Science and Engineering Forum