| Date | Speaker | Title |
|---|---|---|
| January 3 | Cesar Oliveira | Catalytic Activity of the Serine Protease of Human Cytomegalovirus: A Theoretical Study |
| January 10 | Eduard Mateescu | Nutrition-induced Growth Regulation of the Bacterial Cell Cycle |
| January 17 | Chia-En Chang | Brownian Dynamics Simulations in a Coarse-Grained Model: Gated Binding of Ligands to HIV-1 Protease |
| January 24 | - | No Group Meeting |
| January 31 | - | No Group Meeting |
| February 7 | Kay Hamacher | Assembly of the smaller ribosomal subunit - reduced model computations |
| February 14 | Joachim Dzubiella | Coupling of nonpolar and polar solvation in implicit solvent models |
| February 21 | Jennifer Bui | Protein Binding Mechanism: Fast Conformational Transitions of Neurotoxin Fasciculin-2 upon binding to Acetylcholinesterase |
| February 28 | Jie Liu | Construction of Transcription Modules |
| March 7 | Justin Gullingsrud | Allosteric activation of protein kinase A |
| March 14 | Xiao-Lin Cheng | Molecular Dynamics Study of Channel Gating in Nicotinic Acetylcholine Receptors |
| March 21 | - | No Group Meeting |
| March 28 | Donald Hamelberg | Long-time protein dynamics and critical role of explicit hydration |
| April 5 | Rommie Amaro | Initial Structural and Functional Investigations of an RNA Editing Ligase: Progress Towards a Novel Pharmacophore Model |
| April 12 | John Mongan | Comparison of electric field approximations for calculation of effective Born radii |
| April 19 | - | No Group Meeting |
| April 26 | Yuhui Cheng | TFK+/TFK0 Binding Mechanism Study in Wild-type and H447I mutated mAChE |
| May 3 | - | No Group Meeting |
| May 10 | Jessica MJ Swanson | Characterizing biomolecular recognition and solvation with end-point free energy calculations and implicit solvent models |
| May 17 | David Cerutti | Estimating the Water Density Around Biomolecules (Where the Plot Thickens) |
| May 24 | Cameron Mura | Investigation of the differences between c-Rel and v-Rel |
| May 30 | Zoe Cournia (Heidelberg) | Molecular Dynamics Simulations and Neutron Scattering Calculations of Cholesterol and Biologically-important Sterols in Biomembranes |
| May 31 | - | No Group Meeting |
| June 7 | - | No Group Meeting |
| June 14 | Benzhuo Lu | An order N algorithm for computation of electrostatic interactions in biomolecular system and its application to diffusion process. |
| June 21 | Jesper Sorensen | Molecular Dynamics Simulations of Transthyretin - Free energy calculations providing insight into the amyloid fibril formation |
| June 28 | Tongye Shen | Phosphorylation and folding |
| July 5 | David Minh | The Proper Use of Quasiharmonic Analysis |
| July 12 | Alemayehu Abebe | Structure and dynamics of membrane-bound H-Ras protein |
| July 19 | Ivaylo Ivanov | Origins of Selectivity and Barriers to Ion Translocation in the Nicotinic Acetylcholine and Glycine Receptors |
| July 26 | Barry Grant | 1. An introduction to bio3d: Utilities for the analysis of protein structure and sequence data;2. Investigating the inhibition of a mitotic kinesin: An Eg5 monastrol study |
| August 2 | Tushar Jain | Predicting binding free-energy changes on mutation: Is restrictive sampling the answer? |
| August 9 | Cesar Oliveira | On the Application of Accelerated Molecular Dynamics to Liquid Water Simulations |
| August 16 | Eduard Mateescu | Control of Growth and Replication in Bacteria: Parameter-free Models for the Role of Amino Acid Availability |
| August 23 | Arneh Babakhani | Cell Membrane and Trans-Membrane Protein Phenomena: A Computational Approach |
| August 30 | Chia-En Chang | Configurational Entropy and Binding Pathways: Ligands and HIV-1 Protease Binding Studies |
| September 6 | Justin Gullingsrud | MD investigations of SRPK1 |
| September 13 | - | No Group Meeting |
| September 20 | - | No Group Meeting |
| September 27 | Yong Zhao (Scripps) | FLIPDock: a New Program for Docking Flexible Ligands into Flexible Receptors |
| October 4 | - | No Group Meeting |
| October 11 | Donald Hamelberg | Biological implications of phosphorylation-induced conformational changes |
| October 18 | Rommie Amaro | A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase |
| October 25 | Dana Reichmann (Weizmann) | Protein-Protein Interaction: Architecture and Design of Binding Sites |
| November 1 | David Cerutti | What Lies Between Implicit and Explicit Solvent, or There's so Much Water in this Talk That I had to Keep it Short |
| November 8 | Cameron Mura | Molecular Dynamics of a kB DNA Element |
| November 15 | Xiaolin Cheng | The fast multipole method for electrostatic calculations |
| November 22 | Zeyun Yu | 3D Electron Microscopy Imaging: Applications to Structural Elucidations of Large Bio-molecular Complexes |
| November 29 | Ilja Khavrutskii | Enhanced Harmonic Fourier Beads Method |
| December 6 | Riccardo Baron | Preliminary overview: relaxed complex method / allosteric binding / DNase (Thermo)dynamics / diffusion of macromolecular oxygen in flavoprotein |
| December 13 | Gary Huber | Generic Programming For Molecular Simulations |
| December 20 | - | No Group Meeting |
| December 27 | - | No Group Meeting |