Midwest Quantitative Biology Conference

Table of Contents

Talks - Friday, September 29

Afternoon Session	Page
Shape and Search in Protein Docking, Using Radial Basis Functions by Arthur Olson	1
Molecular Dynamics of apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations by Robert Cukier	2
Role of Conformational Dynamics in Enzymatic Catalysis - A Tale of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase by Honggao Yan	3
Implementing Non-Pairwise Statistical Potentials for Computational Protein Design by Jack Snoeyink	4
Dynamic Clustering in a Model for an Insect's Antennal Lobe by David Terman	5
Resource Quality Dynamics and Its Implications by Yang Kuang	6
Quantitative Modeling of a cis-Regulatory Transcriptional Grammar by David Arnosti	7
Specificity and Robustness in Cell Signaling by Qing Nie	8
Demonstration of Tangible Interfaces for Molecular Biology by Arthur Olson	9

Talks - Saturday, September 30

Morning Session

Simulations of Complex Biological Systems with Quantum Mechanics and Statistical Mechanics by Weitao Yang	10
Knowledge-based Approaches to Predicting Protein Interface Hot Spots by Julie Mitchell	11
A New Paradigm for Biomolecular Electrostatics by Guowei Wei	12
Improving Protein-ligand Scoring Using a Correlation-based Method by Maria Zavodszky	13
Homogenized Limits in Visual Transduction: The Role of the Incisures in the Variability of Single Photon Response by Emmanuele DiBenedetto	14
Temporal and Spatial Specificity of Gene Expression Regulated by Sp1 and Sp3 by Moxun Tang	15
Constraint Counting and Flexibility in Protein Networks by Leslie Kuhn	16

Afternoon Session

Dynamics in Genetic Networks by Leon Glass	17
Stability of Intracellular Growth Factor Complexes by Rami Tzafriri	18
Many Numbers at Many Levels: Intradisciplinary Thoughts on Gene Regulatory Networks by Titus Brown	19
Modeling Signalling Statistics and Selectivity of Cell Death in Heterogeneous Populations by Phillip Duxbury	20

Talks - Sunday, October 1

Morning Session

Nonlinear Dynamics and Systems Biology by Bard Ermentrout	21
Using Molecular Data to Estimate the Evolution of Species - Not Just the Phylogeny of Genes by Dennis Pearl	22
Homology Modeling of a Mixed-Lineage Kinase (MLK3) Involved in Signal Transduction: Theoretical/Experimental Studies by Steve Siebold	23
Computational Methods for Predicting cis-Regulatory Modules by Saurabh Sinha	24
A Framework for Analyzing Topological Folding Barriers in Protein Folding by Todd Yeates	25
Prediction of Lipid Accessibility and Protein-Protein Interaction Sites in Membrane Proteins by Jarek Meller	26
On the Force Dependence of Biomolecular Conformational Kinetics by Ioan Andricioaei	27
Loop Closure Methods for Proteins by Bill Wedemeyer	28

Posters

1.	Two-Dimentional NOESY Nuclear Magnetic Resonance and Molecular Dynamics Study in Conformation Behavior of 2-Octanone in Humic Acid by Yao-Ying chien	29
2.	Understanding Bistability in Complex Enzyme-driven Reaction Networks by Gheorghe Craciun .	30
3.	Graphical Environments for Protein Modeling by Silvia Crivelli	31
4.	Structural analysis of the Influenza and HIV Fusion Proteins By Solid State NMR by Jaime Curtis	32
5.	The KFC Server: A Web Server Using Automated Decision Trees to Predict Protein Interaction Hot Spots by Steven Darnell	33
6.	Computational cis-regulatory Transcriptional Grammar and Developing Predictive Mathematical Models by Walid Fakhouri	34
7.	A Large Number of Novel-Small Open Reading Frames (sORFs) in the Intergenic Regions of the Arabidopsis thalianaGenome are Transcribed or Under Purifying Selection by Kousuke Hanada	35
8.	Monte Carlo Simulation of Pattern Formation of Microtubules and Molecular Motors by Zhiyuan Jia	36
9.	Parameterization for Dynamics of Solvent Molecules Around a Solute by Adnan Khan	37
10.	Study of Effective Drift and Diffusivity for Flashing Ratchets Using Homogenized Equations by Juan Latorre	38
11.	A Boundary Integral Method and Adaptive Treecode for Poisson-Boltzmann Equation by Peijun Li	39
12.	Global Optimization in Protein Docking Using Clustering and Underestimation by Roummel Marcia	40
13.	Modeling Mitochondrial Biogenesis, Transport & Destruction in Neurons by Matthew O'Toole	41
14.	Astroglia-mediated Involvement of Saturated Fatty Acids in the Pathogenesis by Sachin Patil	42
15.	Thermodynamics of mRNA/gRNA Complex Formation in Trypanosoma brucei by Larissa Reifur	43
16.	Finding the Optimal Alignment for Labeled 3D Point sets Describing Surfaces: Applications to Comparing Protein Binding Sites by Jeffrey Van Voorst	44
17.	Kinetic and Dynamic Properties of Yeast Cytosine Deaminase as Revealed by Site-Directed Mutagenesis and Molecular Dynamics Simulation by Jifeng Wang	45
18.	Rate Constant Calculation for Proton Transfer Reaction by Sandy Yang	46
19.	A Novel High-accuracy Poisson-Boltzmann Solver: Applications to Biomolecular Electrostatics by Sining Yu	47
20.	The Minimal Molecular Surface by Shan Zhao	48

Participant List