| Date | Speaker | Title |
|---|---|---|
| January 7 | Yuhui Cheng UCSD |
Insight into Phosphoryl Transfer Mechanism of PKA with High Level ab initio QM/MM calculations and MD simulations |
| January 14 | Richard Henchman UCSD |
Single Molecule Nanosimulation of the Alpha7 Nicotinic Receptor |
| January 21 | Jessica Swanson UCSD |
Optimized radii for continuum solvent calculations; the importance of attentive parameters |
| January 28 | Alex Perryman UCSD |
HIV Protease Drug Resistance |
| February 4 | Dave Cerutti UCSD |
Rapid Approximations to Electrostatic Energy in Protein:Protein Association; Fitting Elephants with Unlimited, Unfounded Parameters |
| February 11 | David Zhang UCSD |
Steered MD study of ligand unbinding in ha7-nAChR |
| February 18 | - | No Group Meeting Biophysical Society Meeting |
| February 25 | Jason Suen UCSD |
Adaptive finite element analysis in molecular electrostatics |
| March 3 | Joanna Trylska UCSD |
1. Calcium binding to Cowpea Chlorotic Mottle Virus 2. Coarse-grained model of the ribosome: molecular dynamics simulations - preliminary tests |
| March 10 | John Mongan UCSD |
Constant pH MD (reprise): Once more, with data |
| March 17 | Julie Schames UCSD |
Further exploration into MMP Inhibitor Design |
| March 24 | Richard Law UCSD |
A Model for Anesthetic Binding to Nicotinic AcetylCholine and GABA Receptors |
| March 31 | - | No Group Meeting --ACS-- |
| April 7 | Sanjib Senapati UCSD |
Finite concentration effects on diffusion controlled reactions |
| April 14 | - | No Group Meeting |
| April 21 | Cameron Mura UCSD |
Getting at the basis of indirect DNA readout by c-Rel and related proteins, Part I |
| April 28 | Stewart Adcock UCSD |
I. A Quick Quick Introduction to the McWiki Wiki II. Allineate: Rapid protein structure alignment |
| May 5 | BenZhou Lu UCSD |
Structure and energetics of the C subunit of PKA during ADP release |
| May 12 | - | No Group Meeting |
| May 19 | - | No Group Meeting |
| May 26 | Tongye Shen UCSD |
Conformation switch induced by multi-phosphorylation: a case study of NFAT regulatory domain |
| June 2 | Justin Gullingsrud UCSD |
PKA; An open and closed case |
| June 9 | BenZhou and Yuhui UCSD |
Joint meeting with Taylor Lab PKA - From simulation to experiment and the path in between. |
| June 16 | Donald Hamelberg UCSD |
Running all atom simulations as fast as real-time: Phosphorylation dependent cis/trans isomerization of proline and many more |
| June 23 | Justin Gullingsrud Richard Henchman Jen Bui |
Modified PB Chalk Talk Converging Jarzynski... Summary of the Biopolymer GRC |
| June 30 | Jen Bui UCSD |
Cool Algorithms from the Snake Tamer's Lair |
| July 7 | - | No Group Meeting |
| July 14 | Robert Konecny UCSD |
Viruses: don't open your email attachments! |
| July 21 | Richard Henchman UCSD |
Bits and bobs of the nicotinic receptor |
| July 28 | - | No Group Meeting |
| July 31 | LJCT Symposium | La Jolla Computational Theory Symposium 9 am - 4 pm in NSB Auditorium |
| August 4 | Dave Cerutti UCSD |
I. GRAPPLING with Free Energy Methodology in Flexible Protein Docking II. A Cornucopia of Problems from the Immunoglobulin Superfamily Conference |
| August 11 | - | No Group Meeting |
| August 18 | - | No Group Meeting Protein Society Meeting - SD,CA |
| August 25 | David Zhang UCSD |
Rate constant calculations for tetrameric mAChE by solving the steady-state Smoluchowski equation using finite element method |
| September 1 | Kay Hamacher UCSD |
Evolution of Two-Component Signal Transduction: Darwinian Romps on Protein-Protein and Protein-Nucleic Acid Binding Energy Landscapes |
| September 8 | Alex Perryman UCSD |
HIV Protease--Old Conclusions Receive New Support |
| September 15 | John Mongan UCSD |
In Search of pH Driven Conformational Change: Adjusting Hydrogen Bonding Strength in GB |
| September 22 | Jie Liu UCSD |
Introduction to constructing yeast transcription networks |
| September 29 | Joanna Trylska UCSD |
Assembly of the Small Ribosomal Subunit - An Implicit Solvent Approach |
| October 6 | - | No Group Meeting |
| October 13 | Rich Law UCSD |
A gating mechanism proposed from a 15ns simulation of a complete human a7 nicotinic acetylcholine receptor model |
| October 20 | Tushar Jain UCSD |
Configurational Bias-based Monte Carlo Methods |
| October 27 | Bob White UCSD |
Pulling a Specificity Code up by the Bootstraps |
| November 3 | Xiao-Lin Cheng UCSD |
Variant REM for Local Structure Refinement Simulations |
| November 8 | Brooks, Case, & McCammon Groups |
Florence Tama (Brooks Lab): Mechanical properties of icosahedral viruses Ross Walker (Case Lab): Refinements of the AMBER force field via the use of multi-dimensional parameter fitting David Cerutti (McCammon Lab): Macromolecular Associations--Solvation, Motion, and Collossal Hubris |
| November 10 | Joachim Dzubiella UCSD |
Water and Ion Permeation of Simple Hydrophobic Nanopores |
| November 17 | Ben-Zhuo Lu UCSD |
An alternative PB solver: The Boundary Elementary Method |
| November 24 | - | No Group Meeting |
| December 1 | Justin Gullingsrud UCSD |
Dynamic binding of PKA regulatory subunits |
| December 8 | - | No Group Meeting |
| December 15 | Cameron Mura UCSD |
Investigation of the physical differences between some Rel proteins & some Sm-like stuff |
| December 22 | - | No Group Meeting |
| December 29 | - | No Group Meeting |