| Date | Speaker | Title |
|---|---|---|
| January 3 | Tongye Shen UCSD |
- |
| January 10 | Alex Perryman UCSD |
- |
| January 17 | Jennifer Bui UCSD |
- |
| January 24 | Stephen Bond UCSD |
Geometric Integrators for Constant Temperature Molecular Dynamics |
| January 31 | Larry Canino UCSD |
Evaluation of Boundary Forces Arising from the Non-linear Poisson-Boltzmann Equation |
| February 7 | Yingkai Zhang UCSD |
Ab Initio QM/MM and Free Energy Calculations on Enzyme Reactions |
| February 14 | Julie Schames UCSD |
Docking Inhibitor Models to MD Snapshots of HIV Integrase |
| February 21 | Dimitri Morikis UCSD |
Proton Transfer Coupled to Native State Conformational Dynamics and Catalysis of GART |
| February 28 | No Group Meeting | - |
| March 6 | Tina D. Poulsen University of Aarhus, Denmark |
Solvent Effects on Electronic Transitions and Molecular Properties |
| March 7 | Richard Henchman UCSD |
Water Dynamics in Acetylcholinesterase |
| March 14 | Haihong Ni UCSD |
MD Simulation Studies on the HIV-1 Integrase-5CITEP Complex |
| March 21 | No Group Meeting | - |
| March 28 | No Group Meeting | - |
| March 29 | Anton Feenstra University of Groningen |
Hierarchy of Protein Motion and Folding |
| April 4 | No Group Meeting | - |
| April 9 | Group Discussion | - |
| April 16 | Jeremy Kua UCSD |
Computational Studies of Heterogeneous Catalysis by Late Transition Metals |
| April 23 | Ernesto Andrianantoandro Salk/UCSD |
Kinetics of End to End Actin Filament Annealing |
| May 4 | Huafeng Xu Columbia University |
P3M Ewald/rRespa and its Application to the Study of Hydrogen Bond Dynamics |
| May 7 | Group Discussion | - |
| May 14 | Johan Ulander University of Houston |
Accessing Macro from Micro, the Decay of Correlation Functions in Ionic Liquids |
| May 15 | Nathan Baker UCSD |
Evaluating the Electrostatic Properties of Cellular Components |
| May 21 | Jesus Izaguirre Notre Dame University |
Longer Timesteps in Molecular Dynamics Simulations |
| May 28 | Dimitri Morikis UCSD |
pKa of PKA |
| June 4 | Stephen Bond UCSD |
Report from the International Conference on Computational Science |
| June 11 | Alexei Podtelezhnikov UCSD |
A Model of IN-DNA Complex Based on Hydrodynamic Properties of HIV-1 Integrase |
| June 18 | No Group Meeting | - |
| June 22 | Simpson Joseph UCSD |
The Ribosome |
| June 25 | Angela Scott UCSD |
PKC |
| July 2 | Tongye Shen UCSD |
Association Rate Calculation with the Steady-State Smoluchowski Equation |
| July 9 | Kaihsu Tai UCSD |
Development in Analyzing the Acetylcholinesterase Trajectories |
| July 16 | Alex Perryman UCSD |
Initial Homology Modeling of the Type II Somatostatin Receptor |
| July 23 | Group Discussion | Various |
| July 30 | Ernst-Walter Knapp Free University of Berlin |
Artificial Cytochrome b: Computer Modeling and Evaluation of Redox Potentials |
| August 6 | Burak Aksoylu UCSD |
Adaptive Multilevel Numerical Methods with Applications in Diffusive Biomolecular Reactions |
| August 9 | Larry Canino UCSD |
Does the GART Activation Loop Helix-Coil Transition have an On-Switch |
| August 13 | Yingkai Zhang UCSD |
Affinity and Dynamics of Molecular Recognition |
| August 16 | Volkhard Helms Max-Planck Institute, Frankfurt |
Green Fluoresent Protein Discussion |
| August 17 | Volkhard Helms Max-Planck Institute, Frankfurt |
Q-HOP MD - Molecular Dynamics Simulations with Quantum Mechanically Derived Proton Hopping |
| August 20 | Jeremy Kua UCSD |
Unfolding of the Helical Region of PKI(5-24) Using Stochastic Dynamics Simulations |
| August 27 | Jung-Hsin Lin UCSD |
Anchoring Mechanisms of C2 Domains |
| September 3 | No Group Meeting | - |
| September 7 | Ben McMahon Los Alamos National Labs |
Informal Protein Kinase Discussion |
| September 10 | Jennifer Bui UCSD |
MD simulation of Acetylcholinesterase/TMA |
| September 17 | Julie Schames UCSD |
The Role of Water and Protein Flexibility in Docking to HIV Integrase |
| September 24 | Richard Henchman UCSD |
More Than You Would Ever Want to Know About Water Around Acetylcholinesterase |
| October 1 | Jung-Hsin Lin UCSD |
Conference Report: Bridging the Time-Scale Gap |
| October 8 | Jens Nielsen UCSD |
An Empirical Force Field and Methods for Predicting Protein Folding Nuclei |
| October 15 | Group Discussion | Research Manuals |
| October 19 | Wonpil Im Cornell |
Ion Permeation Through OmpF Porin From Eschericha Coli: Theoretical Studies Using Molecular Dynamics, Brownian Dynamics, and the Electrodiffusion Theory |
| October 22 | Literature | - |
| October 29 | No Group Meeting | - |
| November 5 | Hugh MacMillan UCSD |
Math is a Beach |
| November 14 | Vassiliki-Alexandra Glezakou SDSC |
Considerations in Non-Adiabatic Chemistry |
| November 16 | Robert S. Eisenberg Rush Medical Center, Chicago |
Selectivity in Ionic Channels: Electrostatics and Entropics of Confined Charged Spheres |
| November 19 | Julie Mitchell SDSC |
Atomic Density Methods for Characterizing Molecular Shape and Shape Complementarity |
| November 26 | Group Discussion | Research Manuals |
| December 3 | Robert Konecny UCSD |
Theoretical Insights into Mechanism of Silica Pathogenicity |
| December 10 | No Group Meeting | - |
| December 17 | No Group Meeting | - |